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* |
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* Created by Charles F. Vardeman II on 11/26/05. |
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* @author Charles F. Vardeman II |
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* @version $Id: RhoZ.cpp,v 1.2 2006-01-09 22:14:32 tim Exp $ |
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* @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $ |
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* |
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*/ |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int len, int nrbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){ |
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RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nZBins_(nzbins){ |
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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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} |
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deltaR_ = len_ /nRBins_; |
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// fixed number of bins |
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sliceSDLists_.resize(nZBins_); |
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density_.resize(nZBins_); |
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sliceSDLists_.resize(nRBins_); |
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density_.resize(nRBins_); |
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setOutputName(getPrefix(filename) + ".RhoZ"); |
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} |
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void RhoZ::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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StuntDouble* sd; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames / step_; |
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nProcessed_ = nFrames/step_; |
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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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StuntDouble* sd; |
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int i; |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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double sliceVolume = currentSnapshot_->getVolume() /nRBins_; |
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//assume simulation box will never change |
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//Mat3x3d hmat = currentSnapshot_->getHmat(); |
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double halfBoxZ = len_ /2; |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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//wrap the stuntdoubles into a cell |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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currentSnapshot_->wrapVector(pos); |
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sd->setPos(pos); |
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} |
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int i; |
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for (i=0; i < nZBins_; i++) { |
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sliceSDLists_[i].clear(); |
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} |
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//determine which atom belong to which slice |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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int binNo = (pos.z() + halfBoxZ) /deltaR_; |
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sliceSDLists_[binNo].push_back(sd); |
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} |
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RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_; |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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zBox_.push_back(hmat(2,2)); |
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RealType halfBoxZ_ = hmat(2,2) / 2.0; |
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//loop over the slices to calculate the densities |
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for (std::size_t j = 0; j < sliceSDLists_.size(); ++j) { |
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double totalMass = 0; |
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for (int k = 0; k < sliceSDLists_[j].size(); ++k) { |
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totalMass += sliceSDLists_[j][k]->getMass(); |
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} |
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density_[j] += totalMass/sliceVolume; |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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//wrap the stuntdoubles into a cell |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(pos); |
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sd->setPos(pos); |
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} |
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|
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//determine which atom belongs to which slice |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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// shift molecules by half a box to have bins start at 0 |
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int binNo = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2)); |
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sliceSDLists_[binNo].push_back(sd); |
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} |
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//loop over the slices to calculate the densities |
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for (i = 0; i < nZBins_; i++) { |
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RealType totalMass = 0; |
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for (int k = 0; k < sliceSDLists_[i].size(); ++k) { |
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totalMass += sliceSDLists_[i][k]->getMass(); |
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} |
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density_[i] += totalMass/sliceVolume; |
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} |
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} |
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writeDensity(); |
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} |
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void RhoZ::writeDensity() { |
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// compute average box length: |
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std::vector<RealType>::iterator j; |
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RealType zSum = 0.0; |
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for (j = zBox_.begin(); j != zBox_.end(); ++j) { |
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zSum += *j; |
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} |
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RealType zAve = zSum / zBox_.size(); |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#RhoZ\n"; |
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rdfStream << "#selection: (" << selectionScript_ << ")\t"; |
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rdfStream << "#nFrames:\t" << nProcessed_ << "\n"; |
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rdfStream << "#selection: (" << selectionScript_ << ")\n"; |
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rdfStream << "#z\tdensity\n"; |
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for (int i = 0; i < density_.size(); ++i) { |
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double r = deltaR_ * (i + 0.5); |
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rdfStream << r << "\t" << density_[i]/nProcessed_ << "\n"; |
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RealType z = zAve * (i+0.5)/density_.size(); |
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rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n"; |
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} |
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} else { |
