--- trunk/src/applications/staticProps/RadialDistrFunc.cpp 2005/02/09 18:12:47 307 +++ trunk/src/applications/staticProps/RadialDistrFunc.cpp 2005/02/17 18:30:54 361 @@ -42,57 +42,111 @@ #include #include "RadialDistrFunc.hpp" - +#include "io/DumpReader.hpp" +#include "primitives/Molecule.hpp" namespace oopse { -RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len) - : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1), - selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info){ +RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) + : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), + selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), + seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ evaluator1_.loadScriptString(sele1); evaluator2_.loadScriptString(sele2); - if (!evaluator1_->isDynamic()) { - seleMan1_.setSelectionSet(evaluator1_->evaluate()); + if (!evaluator1_.isDynamic()) { + seleMan1_.setSelectionSet(evaluator1_.evaluate()); + validateSelection1(seleMan1_); } - if (!evaluator2_->isDynamic()) { - seleMan2_.setSelectionSet(evaluator2_->evaluate()); + if (!evaluator2_.isDynamic()) { + seleMan2_.setSelectionSet(evaluator2_.evaluate()); + validateSelection2(seleMan2_); } - delta_ = len_ /nbins_; + if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { + //if all selections are static, we can precompute the number of real pairs + common_ = seleMan1_ & seleMan2_; + sele1_minus_common_ = seleMan1_ - common_; + sele2_minus_common_ = seleMan2_ - common_; + + int nSelected1 = seleMan1_.getSelectionCount(); + int nSelected2 = seleMan2_.getSelectionCount(); + int nIntersect = common_.getSelectionCount(); + + nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; + } + } void RadialDistrFunc::process() { - + Molecule* mol; + RigidBody* rb; + SimInfo::MoleculeIterator mi; + Molecule::RigidBodyIterator rbIter; + preProcess(); DumpReader reader(info_, dumpFilename_); - int nFrames = reader->getNFrames(); - nProcessed_ = nFrames / step_ + 1; + int nFrames = reader.getNFrames(); + nProcessed_ = nFrames / step_; + for (int i = 0; i < nFrames; i += step_) { - reader->readFrame(i); + reader.readFrame(i); currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); - if (evaluator1_->isDynamic()) { - seleMan1_.setSelectionSet(evaluator1_->evaluate()); + if (evaluator1_.isDynamic()) { + seleMan1_.setSelectionSet(evaluator1_.evaluate()); + validateSelection1(seleMan1_); } - if (evaluator2_->isDynamic()) { - seleMan2_.setSelectionSet(evaluator2_->evaluate()); + if (evaluator2_.isDynamic()) { + seleMan2_.setSelectionSet(evaluator2_.evaluate()); + validateSelection2(seleMan2_); } + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + + //change the positions of atoms which belong to the rigidbodies + for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + rb->updateAtoms(); + } + } + initalizeHistogram(); - StuntDouble* sd1; - int j; - for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) { - StuntDouble* sd2; - int k; - for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) { - collectHistogram(sd1, sd2); - } + + //selections may overlap. + // + // |s1 -c | c | + // | c |s2 - c| + // + // s1 : number of selected stuntdoubles in selection1 + // s2 : number of selected stuntdoubles in selection2 + // c : number of intersect stuntdouble between selection1 and selection2 + //when loop over the pairs, we can divide the looping into 3 stages + //stage 1 : [s1-c] [s2] + //stage 2 : [c] [s2 - c] + //stage 3 : [c] [c] + //stage 1 and stage 2 are completly non-overlapping + //stage 3 are completely overlapping + + if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { + + common_ = seleMan1_ & seleMan2_; + sele1_minus_common_ = seleMan1_ - common_; + sele2_minus_common_ = seleMan2_ - common_; + int nSelected1 = seleMan1_.getSelectionCount(); + int nSelected2 = seleMan2_.getSelectionCount(); + int nIntersect = common_.getSelectionCount(); + + nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; } + processNonOverlapping(sele1_minus_common_, seleMan2_); + processNonOverlapping(common_, sele2_minus_common_); + processOverlapping(common_); + + processHistogram(); } @@ -102,4 +156,37 @@ void RadialDistrFunc::process() { writeRdf(); } +void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) { + StuntDouble* sd1; + StuntDouble* sd2; + int i; + int j; + + for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) { + + for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { + collectHistogram(sd1, sd2); + } + } + } + +void RadialDistrFunc::processOverlapping( SelectionManager& sman) { + StuntDouble* sd1; + StuntDouble* sd2; + int i; + int j; + + //basically, it is the same as below loop + //for (int i = 0; i < n; ++i ) + // for (int j = i + 1; j < n; ++j) {} + + for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) { + for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) { + collectHistogram(sd1, sd2); + } + } + +} + +}