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

Comparing trunk/src/selection/HullFinder.cpp (file contents):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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	>
57	>	stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
58	>	bonds_.resize(nObjects_[BOND]);
59	>	bends_.resize(nObjects_[BEND]);
60	>	torsions_.resize(nObjects_[TORSION]);
61	>	inversions_.resize(nObjects_[INVERSION]);
62
63		SimInfo::MoleculeIterator mi;
64	<	Molecule* mol;
55	<	StuntDouble* integrableObject;
56	<	Molecule::IntegrableObjectIterator  ioi;
64	>	Molecule::IntegrableObjectIterator ioi;
65		Molecule::AtomIterator ai;
58	–	Atom* atom;
66		Molecule::RigidBodyIterator rbIter;
67	<	RigidBody* rb;
67	>	Molecule::BondIterator bondIter;
68	>	Molecule::BendIterator bendIter;
69	>	Molecule::TorsionIterator torsionIter;
70	>	Molecule::InversionIterator inversionIter;
71
72	+	Molecule* mol;
73	+	StuntDouble* sd;
74	+	Atom* atom;
75	+	RigidBody* rb;
76	+	Bond* bond;
77	+	Bend* bend;
78	+	Torsion* torsion;
79	+	Inversion* inversion;
80	+
81		for (mol = info_->beginMolecule(mi); mol != NULL;
82		mol = info_->nextMolecule(mi)) {
83
84		// Hull is constructed from all known integrable objects.
85	<	for (integrableObject = mol->beginIntegrableObject(ioi);
86	<	integrableObject != NULL;
87	<	integrableObject = mol->nextIntegrableObject(ioi)) {
88	<	localSites_.push_back(integrableObject);
85	>	for (sd = mol->beginIntegrableObject(ioi);
86	>	sd != NULL;
87	>	sd = mol->nextIntegrableObject(ioi)) {
88	>	localSites_.push_back(sd);
89		}
90
91		// selection can include atoms (which may be a subset of the IOs)
#	Line 80 | Line 99 | namespace OpenMD {
99		rb = mol->nextRigidBody(rbIter)) {
100		stuntdoubles_[rb->getGlobalIndex()] = rb;
101		}
102	<
103	<	}
104	<	surfaceMesh_ = new ConvexHull();
102	>
103	>	// These others are going to be inferred from the objects on the hull:
104	>	for (bond = mol->beginBond(bondIter); bond != NULL;
105	>	bond = mol->nextBond(bondIter)) {
106	>	bonds_[bond->getGlobalIndex()] = bond;
107	>	}
108	>	for (bend = mol->beginBend(bendIter); bend != NULL;
109	>	bend = mol->nextBend(bendIter)) {
110	>	bends_[bend->getGlobalIndex()] = bend;
111	>	}
112	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
113	>	torsion = mol->nextTorsion(torsionIter)) {
114	>	torsions_[torsion->getGlobalIndex()] = torsion;
115	>	}
116	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
117	>	inversion = mol->nextInversion(inversionIter)) {
118	>	inversions_[inversion->getGlobalIndex()] = inversion;
119	>	}
120	>
121	>	}
122	>	#ifdef HAVE_QHULL
123	>	surfaceMesh_ = new ConvexHull();
124	>	#endif
125		}
126
127	<	OpenMDBitSet HullFinder::findHull() {
128	<	StuntDouble* sd;
129	<	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
91	<	OpenMDBitSet bsResult(nStuntDoubles_);
127	>	HullFinder::~HullFinder() {
128	>	delete surfaceMesh_;
129	>	}
130
131	+	SelectionSet HullFinder::findHull() {
132	+	SelectionSet ssResult(nObjects_);
133	+	#ifdef HAVE_QHULL
134		surfaceMesh_->computeHull(localSites_);
135	+	#else
136	+	sprintf( painCave.errMsg,
137	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
138	+	"\tPlease rebuild OpenMD with qhull enabled.");
139	+	painCave.severity = OPENMD_ERROR;
140	+	painCave.isFatal = 1;
141	+	simError();
142	+	#endif
143	+
144		std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
95	–	int nTriangles = sMesh.size();
145		// Loop over the mesh faces
146		std::vector<Triangle>::iterator face;
147		std::vector<StuntDouble*>::iterator vertex;
148
149	+	// This will work in parallel because the triangles returned by the mesh
150	+	// have a NULL stuntDouble if this processor doesn't own the
151	+
152		for (face = sMesh.begin(); face != sMesh.end(); ++face) {
153		Triangle thisTriangle = *face;
154		std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
155		for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
156		if ((*vertex) != NULL) {
157	<	bsResult.setBitOn((*vertex)->getGlobalIndex());
157	>	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
158		}
159		}
160		}
161	<	return bsResult;
161	>	return ssResult;
162		}
163
164	+	SelectionSet HullFinder::findHull(int frame) {
165	+	SelectionSet ssResult(nObjects_);
166	+	#ifdef HAVE_QHULL
167	+	surfaceMesh_->computeHull(localSites_);
168	+	#else
169	+	sprintf( painCave.errMsg,
170	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
171	+	"\tPlease rebuild OpenMD with qhull enabled.");
172	+	painCave.severity = OPENMD_ERROR;
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	#endif
176	+
177	+	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
178	+	// Loop over the mesh faces
179	+	std::vector<Triangle>::iterator face;
180	+	std::vector<StuntDouble*>::iterator vertex;
181	+
182	+	// This will work in parallel because the triangles returned by the mesh
183	+	// have a NULL stuntDouble if this processor doesn't own the
184	+
185	+	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
186	+	Triangle thisTriangle = *face;
187	+	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
188	+	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
189	+	if ((*vertex) != NULL) {
190	+	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
191	+	}
192	+	}
193	+	}
194	+	surfaceArea_ = surfaceMesh_->getArea();
195	+	return ssResult;
196	+	}
197	+
198		}

Comparing trunk/src/selection/HullFinder.cpp (property svn:keywords):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 0 | Line 1
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