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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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using namespace std; |
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namespace OpenMD { |
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1) |
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: StaticAnalyser(info, filename), doVect_(true), |
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selectionScript1_(sele1), evaluator1_(info), |
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evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
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setOutputName(getPrefix(filename) + ".p2"); |
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evaluator1_.loadScriptString(sele1); |
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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} |
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P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info){ |
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1, const string& sele2) |
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: StaticAnalyser(info, filename), doVect_(false), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
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evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
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setOutputName(getPrefix(filename) + ".p2"); |
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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}else { |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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}else { |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
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sprintf( painCave.errMsg, |
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"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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int i; |
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int j; |
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StuntDouble* sd1; |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
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sdPairs_.push_back(std::make_pair(sd1, sd2)); |
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} |
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sdPairs_.push_back(make_pair(sd1, sd2)); |
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} |
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} |
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void P2OrderParameter::process() { |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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StuntDouble* sd; |
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int i, ii; |
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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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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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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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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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} |
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Mat3x3d orderTensor(0.0); |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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orderTensor +=outProduct(vec, vec); |
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if (doVect_) { |
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if (evaluator1_.isDynamic()) |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
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sd = seleMan1_.nextSelected(ii)) { |
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if (sd->isDirectional()) { |
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Vector3d vec = sd->getA().getColumn(2); |
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vec.normalize(); |
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orderTensor += outProduct(vec, vec); |
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} |
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} |
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orderTensor /= seleMan1_.getSelectionCount(); |
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} else { |
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for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); |
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j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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orderTensor +=outProduct(vec, vec); |
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} |
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orderTensor /= sdPairs_.size(); |
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} |
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orderTensor /= sdPairs_.size(); |
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orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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Vector3d eigenvalues; |
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Mat3x3d eigenvectors; |
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Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
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int which; |
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} |
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RealType angle = 0.0; |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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angle += acos(dot(vec, director)) ; |
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RealType p4 = 0.0; |
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if (doVect_) { |
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for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
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sd = seleMan1_.nextSelected(ii)) { |
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if (sd->isDirectional()) { |
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Vector3d vec = sd->getA().getColumn(2); |
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vec.normalize(); |
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RealType myDot = dot(vec, director); |
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angle += acos(myDot); |
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p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
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} |
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} |
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angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0; |
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p4 /= (seleMan1_.getSelectionCount()); |
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} else { |
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for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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RealType myDot = dot(vec, director); |
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angle += acos(myDot); |
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p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
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} |
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angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
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p4 /= (seleMan1_.getSelectionCount()); |
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} |
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angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
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OrderParam param; |
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param.p2 = p2; |
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param.director = director; |
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param.angle = angle; |
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param.p4 = p4; |
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orderParams_.push_back(param); |
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} |
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writeP2(); |
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} |
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void P2OrderParameter::writeP2() { |
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std::ofstream os(getOutputFileName().c_str()); |
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ofstream os(getOutputFileName().c_str()); |
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os << "#radial distribution function\n"; |
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os<< "#selection1: (" << selectionScript1_ << ")\t"; |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
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if (!doVect_) { |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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} |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\t<p4>\n"; |
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for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
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for (size_t i = 0; i < orderParams_.size(); ++i) { |
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os << orderParams_[i].p2 << "\t" |
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<< orderParams_[i].director[0] << "\t" |
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<< orderParams_[i].director[1] << "\t" |
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<< orderParams_[i].director[2] << "\t" |
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<< orderParams_[i].angle << "\n"; |
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<< orderParams_[i].angle << "\t" |
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<< orderParams_[i].p4 << "\n"; |
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} |
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