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* |
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* NanoVolume.cpp |
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* |
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* Purpose: To calculate convexhull, hull volume and radius |
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* using the CGAL library. |
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* |
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* Created by Charles F. Vardeman II on 14 Dec 2006. |
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* @author Charles F. Vardeman II |
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< |
* @version $Id: NanoVolume.cpp,v 1.1 2007-09-17 20:11:47 chuckv Exp $ |
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> |
* @version $Id: NanoVolume.cpp,v 1.9 2009-10-22 14:19:26 gezelter Exp $ |
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* |
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*/ |
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const std::string& filename, |
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const std::string& sele) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) { |
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setOutputName(getPrefix(filename) + ".off"); |
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setOutputName(getPrefix(filename) + ".avol"); |
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|
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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frameCounter_ = 0; |
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totalVolume_ = 0.0; |
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} |
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|
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void NanoVolume::process() { |
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< |
|
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> |
#if defined(HAVE_QHULL) |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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Vector3d vec; |
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int i,j; |
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|
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ConvexHull* hull = new ConvexHull(); |
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#ifdef HAVE_QHULL |
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> |
ConvexHull* thishull = new ConvexHull(); |
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> |
#endif |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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|
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< |
pos_.reserve(info_->getNGlobalAtoms()); |
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> |
theAtoms_.reserve(info_->getNGlobalAtoms()); |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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// Clear pos vector between each frame. |
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pos_.clear(); |
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> |
theAtoms_.clear(); |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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// outer loop is over the selected StuntDoubles: |
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|
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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> |
sd = seleMan_.nextSelected(i)) { |
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|
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pos_.push_back(sd->getPos()); |
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theAtoms_.push_back(sd); |
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myIndex = sd->getGlobalIndex(); |
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|
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} |
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+ |
|
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+ |
/* |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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theAtoms_.push_back(atom); |
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} |
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} |
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*/ |
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// Generate convex hull for this frame. |
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hull->genHull(pos_); |
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< |
// RealType hullVolume = hull->getVolume(); |
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//std::cout <<"The volume for this hull is: "<< hullVolume << std::endl; |
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< |
|
| 137 |
> |
thishull->computeHull(theAtoms_); |
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> |
// totalVolume_ += hull->getVolume(); |
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} |
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+ |
//RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
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+ |
//std::cout.precision(7); |
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//std::cout << avgVolume << std::endl; |
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/* |
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std::ofstream osq(getOutputFileName().c_str()); |
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+ |
osq.precision(7); |
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if (osq.is_open()){ |
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osq << avgVolume << std::endl; |
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+ |
|
| 149 |
+ |
} |
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+ |
osq.close(); |
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*/ |
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#else |
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+ |
sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); |
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+ |
painCave.isFatal = 1; |
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+ |
simError(); |
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|
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+ |
#endif |
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+ |
|
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} |
