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*/ |
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#include <algorithm> |
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#include <functional> |
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#include "applications/staticProps/DensityPlot.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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namespace oopse { |
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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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DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType 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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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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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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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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int i; |
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for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1); |
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int k; |
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for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) { |
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if (!sd->isAtom()) { |
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simError(); |
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} |
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double nelectron = doubleData->getData(); |
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RealType nelectron = doubleData->getData(); |
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data = atom->getAtomType()->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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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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RealType sigma = ljParam.sigma * 0.5; |
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RealType 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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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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RealType 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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RealType 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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} |
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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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std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed)); |
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writeDensity(); |
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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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> |
RealType 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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RealType mass = sd->getMass(); |
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totalMass += mass; |
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newOrigin += sd->getPos() * mass; |
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} |