--- trunk/src/applications/staticProps/RadialDistrFunc.cpp 2005/02/15 19:36:07 351 +++ trunk/src/applications/staticProps/RadialDistrFunc.cpp 2008/01/23 21:21:50 1213 @@ -46,36 +46,39 @@ namespace oopse { #include "primitives/Molecule.hpp" namespace oopse { -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){ + RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) + : StaticAnalyser(info, filename), + 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); + evaluator1_.loadScriptString(sele1); + evaluator2_.loadScriptString(sele2); - if (!evaluator1_.isDynamic()) { - seleMan1_.setSelectionSet(evaluator1_.evaluate()); - } - if (!evaluator2_.isDynamic()) { - seleMan2_.setSelectionSet(evaluator2_.evaluate()); - } + if (!evaluator1_.isDynamic()) { + seleMan1_.setSelectionSet(evaluator1_.evaluate()); + validateSelection1(seleMan1_); + } + if (!evaluator2_.isDynamic()) { + seleMan2_.setSelectionSet(evaluator2_.evaluate()); + validateSelection2(seleMan2_); + } - if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { + 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(); - - BitSet bs = seleMan1_.getSelectionSet(); - bs &= seleMan2_.getSelectionSet(); - int nIntersect = bs.countBits(); - - nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; - } + int nIntersect = common_.getSelectionCount(); + + nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; + } -} + } -void RadialDistrFunc::process() { + void RadialDistrFunc::process() { Molecule* mol; RigidBody* rb; SimInfo::MoleculeIterator mi; @@ -88,63 +91,99 @@ void RadialDistrFunc::process() { nProcessed_ = nFrames / step_; for (int i = 0; i < nFrames; i += step_) { - reader.readFrame(i); - currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); + reader.readFrame(i); + currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); - if (evaluator1_.isDynamic()) { - seleMan1_.setSelectionSet(evaluator1_.evaluate()); - } - if (evaluator2_.isDynamic()) { - seleMan2_.setSelectionSet(evaluator2_.evaluate()); - } + if (evaluator1_.isDynamic()) { + seleMan1_.setSelectionSet(evaluator1_.evaluate()); + validateSelection1(seleMan1_); + } + if (evaluator2_.isDynamic()) { + seleMan2_.setSelectionSet(evaluator2_.evaluate()); + validateSelection2(seleMan2_); + } - for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + 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(); - } - } + //change the positions of atoms which belong to the rigidbodies + for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + rb->updateAtoms(); + } + } - initalizeHistogram(); + 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)) { - if (sd1 != sd2) { - 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 - processHistogram(); + 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(); } postProcess(); writeRdf(); -} + } -int RadialDistrFunc::getNRealPairs() { - if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { - //if one of the selection is dynamic, need to recompute it + 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)) { - int nSelected1 = seleMan1_.getSelectionCount(); - int nSelected2 = seleMan2_.getSelectionCount(); + for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { + collectHistogram(sd1, sd2); + } + } - BitSet bs = seleMan1_.getSelectionSet(); - bs &= seleMan2_.getSelectionSet(); - int nIntersect = bs.countBits(); + } - nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; + 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); + } } - return nRealPairs_; -} + } }