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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 1816 by gezelter, Fri Dec 7 18:33:33 2012 UTC

#	Line 36 | Line 36
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).
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();
88	+	#endif
89	+	}
90	+
91	+	OpenMDBitSet HullFinder::findHull() {
92	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
93	+	OpenMDBitSet bsResult(nStuntDoubles_);
94	+	#ifdef HAVE_QHULL
95	+	surfaceMesh_->computeHull(localSites_);
96		#else
97		sprintf( painCave.errMsg,
98	<	"Hullfinder error: Hull calculation not possible without libqhull.\n",
99	<	"Please rebuild with Qhull");
98	>	"HullFinder : Hull calculation is not possible without libqhull.\n"
99	>	"\tPlease rebuild OpenMD with qhull enabled.");
100		painCave.severity = OPENMD_ERROR;
101		painCave.isFatal = 1;
102		simError();
94	–
103		#endif
104	+
105	+	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
106	+	int nTriangles = sMesh.size();
107	+	// Loop over the mesh faces
108	+	std::vector<Triangle>::iterator face;
109	+	std::vector<StuntDouble*>::iterator vertex;
110	+
111	+	// This will work in parallel because the triangles returned by the mesh
112	+	// have a NULL stuntDouble if this processor doesn't own the
113	+
114	+	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
115	+	Triangle thisTriangle = *face;
116	+	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
117	+	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
118	+	if ((*vertex) != NULL) {
119	+	bsResult.setBitOn((*vertex)->getGlobalIndex());
120	+	}
121	+	}
122	+	}
123	+	return bsResult;
124		}
125
126	<	OpenMDBitSet HullFinder::findHull() {
127	<	StuntDouble* sd;
100	<	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
126	>	OpenMDBitSet HullFinder::findHull(int frame) {
127	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
128		OpenMDBitSet bsResult(nStuntDoubles_);
129	<
129	>	#ifdef HAVE_QHULL
130		surfaceMesh_->computeHull(localSites_);
131	+	#else
132	+	sprintf( painCave.errMsg,
133	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
134	+	"\tPlease rebuild OpenMD with qhull enabled.");
135	+	painCave.severity = OPENMD_ERROR;
136	+	painCave.isFatal = 1;
137	+	simError();
138	+	#endif
139	+
140		std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
141		int nTriangles = sMesh.size();
142		// Loop over the mesh faces
143		std::vector<Triangle>::iterator face;
144		std::vector<StuntDouble*>::iterator vertex;
145
146	+	// This will work in parallel because the triangles returned by the mesh
147	+	// have a NULL stuntDouble if this processor doesn't own the
148	+
149		for (face = sMesh.begin(); face != sMesh.end(); ++face) {
150		Triangle thisTriangle = *face;
151		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 1816 by gezelter, Fri Dec 7 18:33:33 2012 UTC

#	Line 0 | Line 1
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