# | Line 40 | Line 40 | |
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40 | * | |
41 | * NanoVolume.cpp | |
42 | * | |
43 | – | * Purpose: To calculate convexhull, hull volume and radius |
44 | – | * using the CGAL library. |
45 | – | * |
43 | * Created by Charles F. Vardeman II on 14 Dec 2006. | |
44 | * @author Charles F. Vardeman II | |
45 | < | * @version $Id: NanoVolume.cpp,v 1.3 2007-12-06 19:52:11 chuckv Exp $ |
45 | > | * @version $Id: NanoVolume.cpp,v 1.9 2009-10-22 14:19:26 gezelter Exp $ |
46 | * | |
47 | */ | |
48 | ||
# | Line 73 | Line 70 | void NanoVolume::process() { | |
70 | } | |
71 | ||
72 | void NanoVolume::process() { | |
73 | < | |
73 | > | #if defined(HAVE_QHULL) |
74 | Molecule* mol; | |
75 | Atom* atom; | |
76 | RigidBody* rb; | |
# | Line 85 | Line 82 | void NanoVolume::process() { | |
82 | Vector3d vec; | |
83 | int i,j; | |
84 | ||
85 | < | ConvexHull* hull = new ConvexHull(); |
85 | > | #ifdef HAVE_QHULL |
86 | > | ConvexHull* thishull = new ConvexHull(); |
87 | > | #endif |
88 | ||
89 | DumpReader reader(info_, dumpFilename_); | |
90 | int nFrames = reader.getNFrames(); | |
91 | frameCounter_ = 0; | |
92 | ||
93 | < | pos_.reserve(info_->getNGlobalAtoms()); |
93 | > | theAtoms_.reserve(info_->getNGlobalAtoms()); |
94 | ||
95 | for (int istep = 0; istep < nFrames; istep += step_) { | |
96 | reader.readFrame(istep); | |
# | Line 99 | Line 98 | void NanoVolume::process() { | |
98 | currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); | |
99 | ||
100 | // Clear pos vector between each frame. | |
101 | < | pos_.clear(); |
101 | > | theAtoms_.clear(); |
102 | ||
103 | if (evaluator_.isDynamic()) { | |
104 | seleMan_.setSelectionSet(evaluator_.evaluate()); | |
# | Line 118 | Line 117 | void NanoVolume::process() { | |
117 | // outer loop is over the selected StuntDoubles: | |
118 | ||
119 | for (sd = seleMan_.beginSelected(i); sd != NULL; | |
120 | < | sd = seleMan_.nextSelected(i)) { |
120 | > | sd = seleMan_.nextSelected(i)) { |
121 | ||
122 | < | pos_.push_back(sd->getPos()); |
122 | > | theAtoms_.push_back(sd); |
123 | myIndex = sd->getGlobalIndex(); | |
124 | ||
125 | } | |
126 | + | |
127 | + | /* |
128 | + | for (mol = info_->beginMolecule(mi); mol != NULL; |
129 | + | mol = info_->nextMolecule(mi)) { |
130 | + | for (atom = mol->beginAtom(ai); atom != NULL; |
131 | + | atom = mol->nextAtom(ai)) { |
132 | + | theAtoms_.push_back(atom); |
133 | + | } |
134 | + | } |
135 | + | */ |
136 | // Generate convex hull for this frame. | |
137 | < | hull->genHull(pos_); |
138 | < | totalVolume_ += hull->getVolume(); |
137 | > | thishull->computeHull(theAtoms_); |
138 | > | // totalVolume_ += hull->getVolume(); |
139 | } | |
140 | < | RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
140 | > | //RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
141 | //std::cout.precision(7); | |
142 | //std::cout << avgVolume << std::endl; | |
143 | < | |
143 | > | /* |
144 | std::ofstream osq(getOutputFileName().c_str()); | |
145 | osq.precision(7); | |
146 | if (osq.is_open()){ | |
# | Line 139 | Line 148 | void NanoVolume::process() { | |
148 | ||
149 | } | |
150 | osq.close(); | |
151 | + | */ |
152 | + | #else |
153 | + | sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); |
154 | + | painCave.isFatal = 1; |
155 | + | simError(); |
156 | ||
157 | + | #endif |
158 | + | |
159 | } |
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