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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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|
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) { |
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setOutputName(getPrefix(filename) + ".gxyz"); |
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) { |
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setOutputName(getPrefix(filename) + ".gxyz"); |
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|
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deltaR_ = len_ / nRBins_; |
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evaluator3_.loadScriptString(sele3); |
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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|
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deltaR_ = len_ / nRBins_; |
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|
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histogram_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nRBins_); |
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for(int j = 0; j < nRBins_; ++j) { |
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histogram_[i][j].resize(nRBins_); |
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histogram_[i][j].resize(nRBins_); |
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} |
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} |
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} |
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|
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} |
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|
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//create atom2Mol mapping (should be other class' responsibility) |
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atom2Mol_.insert(atom2Mol_.begin(), info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), static_cast<Molecule*>(NULL)); |
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|
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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atom2Mol_[atom->getGlobalIndex()] = mol; |
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} |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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atom2Mol_[rb->getGlobalIndex()] = mol; |
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} |
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|
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} |
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} |
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|
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void GofXyz::preProcess() { |
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void GofXyz::preProcess() { |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nRBins_); |
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for(int j = 0; j < nRBins_; ++j) { |
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std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
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} |
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histogram_[i].resize(nRBins_); |
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for(int j = 0; j < nRBins_; ++j) { |
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std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
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} |
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} |
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} |
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} |
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void GofXyz::initalizeHistogram() { |
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void GofXyz::initalizeHistogram() { |
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//calculate the center of mass of the molecule of selected stuntdouble in selection1 |
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//determine the new coordinate set of selection1 |
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//v1 = Rs1 -Rcom, |
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//z = Rs1.dipole |
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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|
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assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount()); |
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|
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//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane |
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//v1 = s3 -s1, |
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//z = origin.dipole |
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//x = v1 X z |
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//y = z X x |
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coorSets_.clear(); |
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rotMats_.clear(); |
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int i; |
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StuntDouble* sd; |
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for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) { |
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Vector3d rcom = getMolCom(sd); |
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Vector3d rs1 = sd->getPos(); |
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Vector3d v1 = rcom - rs1; |
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CoorSet currCoorSet; |
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currCoorSet.zaxis = sd->getElectroFrame().getColumn(2); |
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v1.normalize(); |
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currCoorSet.zaxis.normalize(); |
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currCoorSet.xaxis = cross(v1, currCoorSet.zaxis); |
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currCoorSet.yaxis = cross(currCoorSet.zaxis, currCoorSet.xaxis); |
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coorSets_.insert(std::map<int, CoorSet>::value_type(sd->getGlobalIndex(), currCoorSet)); |
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int j; |
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StuntDouble* sd1; |
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StuntDouble* sd3; |
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|
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for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); |
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sd1 != NULL, sd3 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
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|
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Vector3d r3 =sd3->getPos(); |
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Vector3d r1 = sd1->getPos(); |
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Vector3d v1 = r3 - r1; |
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if (usePeriodicBoundaryConditions_) |
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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
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Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
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Vector3d xaxis = cross(v1, zaxis); |
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Vector3d yaxis = cross(zaxis, xaxis); |
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|
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xaxis.normalize(); |
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yaxis.normalize(); |
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zaxis.normalize(); |
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|
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RotMat3x3d rotMat; |
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rotMat.setRow(0, xaxis); |
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rotMat.setRow(1, yaxis); |
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rotMat.setRow(2, zaxis); |
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|
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rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat)); |
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} |
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} |
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} |
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void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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currentSnapshot_->wrapVector(r12); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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std::map<int, CoorSet>::iterator i = coorSets_.find(sd1->getGlobalIndex()); |
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assert(i != coorSets_.end()); |
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std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex()); |
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assert(i != rotMats_.end()); |
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double x = dot(r12, i->second.xaxis); |
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double y = dot(r12, i->second.yaxis); |
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double z = dot(r12, i->second.zaxis); |
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Vector3d newR12 = i->second * r12; |
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// x, y and z's possible values range -halfLen_ to halfLen_ |
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int xbin = (newR12.x()+ halfLen_) / deltaR_; |
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int ybin = (newR12.y() + halfLen_) / deltaR_; |
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int zbin = (newR12.z() + halfLen_) / deltaR_; |
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int xbin = x / deltaR_; |
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int ybin = y / deltaR_; |
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int zbin = z / deltaR_; |
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|
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if (xbin < nRBins_ && ybin < nRBins_ && zbin < nRBins_) { |
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++histogram_[x][y][z]; |
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if (xbin < nRBins_ && xbin >=0 && |
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ybin < nRBins_ && ybin >= 0 && |
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zbin < nRBins_ && zbin >=0 ) { |
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++histogram_[xbin][ybin][zbin]; |
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} |
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} |
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} |
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void GofXyz::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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void GofXyz::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary); |
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if (rdfStream.is_open()) { |
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rdfStream << "#g(x, y, z)\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
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for (int i = 0; i < histogram_.size(); ++i) { |
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//rdfStream << "#g(x, y, z)\n"; |
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//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
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for (int i = 0; i < histogram_.size(); ++i) { |
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for(int j = 0; j < histogram_[i].size(); ++j) { |
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for(int j = 0; j < histogram_[i].size(); ++j) { |
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for(int k = 0;k < histogram_[i].size(); ++k) { |
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|
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rdfStream << histogram_[i][j][k]/nProcessed_ << "\t"; |
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} |
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rdfStream << "\n"; |
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} |
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} |
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for(int k = 0;k < histogram_[i][j].size(); ++k) { |
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rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
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} |
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} |
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} |
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} else { |
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sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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rdfStream.close(); |
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} |
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} |
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Vector3d GofXyz::getMolCom(StuntDouble* sd){ |
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Molecule* mol = atom2Mol_[sd->getGlobalIndex()]; |
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assert(mol); |
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return mol->getCom(); |
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} |
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|
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} |
