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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 1879 by gezelter, Sun Jun 16 15:15:42 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 52 | Line 53 | namespace OpenMD {
53
54		SimInfo::MoleculeIterator mi;
55		Molecule* mol;
56	<	StuntDouble* integrableObject;
56	>	StuntDouble* sd;
57		Molecule::IntegrableObjectIterator  ioi;
58		Molecule::AtomIterator ai;
59		Atom* atom;
#	Line 63 | Line 64 | namespace OpenMD {
64		mol = info_->nextMolecule(mi)) {
65
66		// Hull is constructed from all known integrable objects.
67	<	for (integrableObject = mol->beginIntegrableObject(ioi);
68	<	integrableObject != NULL;
69	<	integrableObject = mol->nextIntegrableObject(ioi)) {
70	<	localSites_.push_back(integrableObject);
67	>	for (sd = mol->beginIntegrableObject(ioi);
68	>	sd != NULL;
69	>	sd = mol->nextIntegrableObject(ioi)) {
70	>	localSites_.push_back(sd);
71		}
72
73		// selection can include atoms (which may be a subset of the IOs)
#	Line 84 | Line 85 | namespace OpenMD {
85		}
86		#ifdef HAVE_QHULL
87		surfaceMesh_ = new ConvexHull();
87	–	#else
88	–	sprintf( painCave.errMsg,
89	–	"Hullfinder error: Hull calculation not possible without libqhull.\n",
90	–	"Please rebuild with Qhull");
91	–	painCave.severity = OPENMD_ERROR;
92	–	painCave.isFatal = 1;
93	–	simError();
94	–
88		#endif
89		}
90
91	+	HullFinder::~HullFinder() {
92	+	delete surfaceMesh_;
93	+	}
94	+
95		OpenMDBitSet HullFinder::findHull() {
99	–	StuntDouble* sd;
100	–	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
96		OpenMDBitSet bsResult(nStuntDoubles_);
97	+	#ifdef HAVE_QHULL
98	+	surfaceMesh_->computeHull(localSites_);
99	+	#else
100	+	sprintf( painCave.errMsg,
101	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
102	+	"\tPlease rebuild OpenMD with qhull enabled.");
103	+	painCave.severity = OPENMD_ERROR;
104	+	painCave.isFatal = 1;
105	+	simError();
106	+	#endif
107	+
108	+	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
109	+	// Loop over the mesh faces
110	+	std::vector<Triangle>::iterator face;
111	+	std::vector<StuntDouble*>::iterator vertex;
112
113	+	// This will work in parallel because the triangles returned by the mesh
114	+	// have a NULL stuntDouble if this processor doesn't own the
115	+
116	+	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
117	+	Triangle thisTriangle = *face;
118	+	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
119	+	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
120	+	if ((*vertex) != NULL) {
121	+	bsResult.setBitOn((*vertex)->getGlobalIndex());
122	+	}
123	+	}
124	+	}
125	+	return bsResult;
126	+	}
127	+
128	+	OpenMDBitSet HullFinder::findHull(int frame) {
129	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
130	+	OpenMDBitSet bsResult(nStuntDoubles_);
131	+	#ifdef HAVE_QHULL
132		surfaceMesh_->computeHull(localSites_);
133	+	#else
134	+	sprintf( painCave.errMsg,
135	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
136	+	"\tPlease rebuild OpenMD with qhull enabled.");
137	+	painCave.severity = OPENMD_ERROR;
138	+	painCave.isFatal = 1;
139	+	simError();
140	+	#endif
141	+
142		std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
143		int nTriangles = sMesh.size();
144		// Loop over the mesh faces
145		std::vector<Triangle>::iterator face;
146		std::vector<StuntDouble*>::iterator vertex;
147
148	+	// This will work in parallel because the triangles returned by the mesh
149	+	// have a NULL stuntDouble if this processor doesn't own the
150	+
151		for (face = sMesh.begin(); face != sMesh.end(); ++face) {
152		Triangle thisTriangle = *face;
153		std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();

Comparing trunk/src/selection/HullFinder.cpp (property svn:keywords):
Revision 1438 by chuckv, Wed Apr 21 19:05:04 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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