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namespace oopse { |
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< |
DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, double len, int nrbins) |
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> |
DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, double len, int nrbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), |
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cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info), |
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len_(len), nRBins_(nrbins), halfLen_(len/2) { |
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setOutputName(getPrefix(filename) + ".density"); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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cmEvaluator_.loadScriptString(cmSele); |
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if (!cmEvaluator_.isDynamic()) { |
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cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate()); |
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} |
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} |
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void DensityPlot::process() { |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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for (int i = 0; i < nFrames; i += step_) { |
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int i; |
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for (i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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} |
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Vector3d cm = info_->getCom(); |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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int i; |
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if (cmEvaluator_.isDynamic()) { |
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cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate()); |
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} |
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Vector3d origin = calcNewOrigin(); |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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double slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1); |
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for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos() - cm; |
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currentSnapshot_->wrapVector(pos); |
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int which = (pos.z() + halfLen_) / deltaR_; |
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if (which < nRBins_ && which >=0 ) { |
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++histogram_[which]; |
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if (!sd->isAtom()) { |
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sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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Atom* atom = static_cast<Atom*>(sd); |
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GenericData* data = atom->getAtomType()->getPropertyByName("nelectron"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (doubleData == NULL) { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to DoubleGenericData\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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double nelectron = doubleData->getData(); |
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data = atom->getAtomType()->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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if (ljData == NULL) { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to LJParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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LJParam ljParam = ljData->getData(); |
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double sigma = ljParam.sigma * 0.5; |
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double sigma2 = sigma * sigma; |
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Vector3d pos = sd->getPos() - origin; |
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/* |
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currentSnapshot_->wrapVector(pos); |
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double wrappedZdist = pos.z() + halfLen_; |
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if (wrappedZdist < 0.0 || wrappedZdist > len_) { |
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continue; |
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} |
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|
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int which =wrappedZdist / deltaR_; |
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density_[which] += nelectron; |
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*/ |
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for (int j =0; j < nRBins_; ++j) { |
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Vector3d tmp(pos); |
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double zdist =j * deltaR_ - halfLen_; |
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tmp[2] += zdist; |
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currentSnapshot_->wrapVector(tmp); |
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double wrappedZdist = tmp.z() + halfLen_; |
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if (wrappedZdist < 0.0 || wrappedZdist > len_) { |
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continue; |
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} |
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int which =wrappedZdist / deltaR_; |
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density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma)); |
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} |
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} |
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} |
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} |
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//std::vector<int>::iterator it = std::max_element(histogram_.begin(), histogram_.end()); |
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//int maxnum = *it; |
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int nProcessed = nFrames / step_; |
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int ntot = info_->getNGlobalAtoms(); |
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int maxnum = ntot * nProcessed; |
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std::transform(histogram_.begin(), histogram_.end(), density_.begin(), std::bind2nd(std::divides<double>(), maxnum)); |
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int nProcessed = nFrames /step_; |
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std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<double>(), nProcessed)); |
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writeDensity(); |
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} |
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Vector3d DensityPlot::calcNewOrigin() { |
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int i; |
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Vector3d newOrigin(0.0); |
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double totalMass = 0.0; |
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for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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double mass = sd->getMass(); |
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totalMass += mass; |
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newOrigin += sd->getPos() * mass; |
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} |
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newOrigin /= totalMass; |
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return newOrigin; |
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} |
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|
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void DensityPlot::writeDensity() { |
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std::ofstream ofs(outputFilename_.c_str(), std::ios::binary); |
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if (ofs.is_open()) { |
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ofs << "#g(x, y, z)\n"; |
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< |
ofs << "#selection: (" << selectionScript_ << ")\t"; |
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< |
ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
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> |
ofs << "#selection: (" << selectionScript_ << ")\n"; |
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> |
ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n"; |
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> |
ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n"; |
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for (int i = 0; i < histogram_.size(); ++i) { |
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ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl; |
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} |
