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#include <algorithm> |
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#include "RadialDistrFunc.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len) |
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: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info){ |
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RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
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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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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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if (!evaluator2_->isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_->evaluate()); |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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deltaR_ = len_ /nbins_; |
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if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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//if all selections are static, we can precompute the number of real pairs |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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BitSet bs = seleMan1_.getSelectionSet(); |
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bs &= seleMan2_.getSelectionSet(); |
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int nIntersect = bs.countBits(); |
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nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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} |
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void RadialDistrFunc::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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preProcess(); |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader->getNFrames(); |
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nProcessed_ = nFrames / step_ + 1; |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames / step_; |
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for (int i = 0; i < nFrames; i += step_) { |
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reader->readFrame(i); |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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if (evaluator1_->isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_->evaluate()); |
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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if (evaluator2_->isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_->evaluate()); |
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if (evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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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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initalizeHistogram(); |
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StuntDouble* sd1; |
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int j; |
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for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) { |
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for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) { |
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StuntDouble* sd2; |
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int k; |
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for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) { |
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collectHistogram(sd1, sd2); |
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for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) { |
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if (sd1 != sd2) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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} |
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writeRdf(); |
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} |
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int RadialDistrFunc::getNRealPairs() { |
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if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
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//if one of the selection is dynamic, need to recompute it |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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BitSet bs = seleMan1_.getSelectionSet(); |
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bs &= seleMan2_.getSelectionSet(); |
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int nIntersect = bs.countBits(); |
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nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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return nRealPairs_; |
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} |
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} |
