--- trunk/src/applications/staticProps/GofRAngle.cpp 2014/09/26 22:22:28 2022 +++ trunk/src/applications/staticProps/GofRAngle.cpp 2014/10/02 14:35:14 2023 @@ -48,22 +48,119 @@ namespace OpenMD { #include "utils/simError.h" namespace OpenMD { + + GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, + const std::string& sele1, + const std::string& sele2, + RealType len, int nrbins, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), len_(len), + nRBins_(nrbins), nAngleBins_(nangleBins), evaluator3_(info), + seleMan3_(info), doSele3_(false) { + + deltaR_ = len_ /(double) nRBins_; + deltaCosAngle_ = 2.0 / (double)nAngleBins_; + histogram_.resize(nRBins_); + avgGofr_.resize(nRBins_); + for (int i = 0 ; i < nRBins_; ++i) { + histogram_[i].resize(nAngleBins_); + avgGofr_[i].resize(nAngleBins_); + } + } + + GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, + const std::string& sele1, + const std::string& sele2, + const std::string& sele3, + RealType len, int nrbins, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), len_(len), + nRBins_(nrbins), nAngleBins_(nangleBins), selectionScript3_(sele3), + evaluator3_(info), seleMan3_(info), doSele3_(true) { - GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, - const std::string& sele2, RealType len, int nrbins, int nangleBins) - : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){ + deltaR_ = len_ /(double) nRBins_; + deltaCosAngle_ = 2.0 / (double)nAngleBins_; + histogram_.resize(nRBins_); + avgGofr_.resize(nRBins_); + for (int i = 0 ; i < nRBins_; ++i) { + histogram_[i].resize(nAngleBins_); + avgGofr_[i].resize(nAngleBins_); + } - deltaR_ = len_ /(double) nRBins_; - deltaCosAngle_ = 2.0 / (double)nAngleBins_; - histogram_.resize(nRBins_); - avgGofr_.resize(nRBins_); - for (int i = 0 ; i < nRBins_; ++i) { - histogram_[i].resize(nAngleBins_); - avgGofr_[i].resize(nAngleBins_); + evaluator3_.loadScriptString(sele3); + if (!evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } + + } + + void GofRAngle::processNonOverlapping( SelectionManager& sman1, + SelectionManager& sman2) { + StuntDouble* sd1; + StuntDouble* sd2; + StuntDouble* sd3; + int i; + int j; + int k; + + // This is the same as a non-overlapping pairwise loop structure: + // for (int i = 0; i < ni ; ++i ) { + // for (int j = 0; j < nj; ++j) {} + // } + + if (doSele3_) { + if (evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); } + if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) { + RadialDistrFunc::processNonOverlapping( sman1, sman2 ); + } + + for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k); + sd1 != NULL && sd3 != NULL; + sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { + for (sd2 = sman2.beginSelected(j); sd2 != NULL; + sd2 = sman2.nextSelected(j)) { + collectHistogram(sd1, sd2, sd3); + } + } + } else { + RadialDistrFunc::processNonOverlapping( sman1, sman2 ); } + } + void GofRAngle::processOverlapping( SelectionManager& sman) { + StuntDouble* sd1; + StuntDouble* sd2; + StuntDouble* sd3; + int i; + int j; + int k; + // This is the same as a pairwise loop structure: + // for (int i = 0; i < n-1 ; ++i ) { + // for (int j = i + 1; j < n; ++j) {} + // } + + if (doSele3_) { + if (evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } + if (sman.getSelectionCount() != seleMan3_.getSelectionCount() ) { + RadialDistrFunc::processOverlapping( sman); + } + for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k); + sd1 != NULL && sd3 != NULL; + sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { + for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; + sd2 = sman.nextSelected(j)) { + collectHistogram(sd1, sd2, sd3); + } + } + } else { + RadialDistrFunc::processOverlapping( sman); + } + } + + void GofRAngle::preProcess() { for (unsigned int i = 0; i < avgGofr_.size(); ++i) { std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); @@ -87,7 +184,8 @@ namespace OpenMD { RealType rLower = i * deltaR_; RealType rUpper = rLower + deltaR_; - RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); + RealType volSlice = ( rUpper * rUpper * rUpper ) - + ( rLower * rLower * rLower ); RealType nIdeal = volSlice * pairConstant; for (unsigned int j = 0; j < histogram_[i].size(); ++j){ @@ -114,6 +212,40 @@ namespace OpenMD { if (distance <= len_) { RealType cosAngle = evaluateAngle(sd1, sd2); + RealType halfBin = (nAngleBins_ - 1) * 0.5; + int whichThetaBin = int(halfBin * (cosAngle + 1.0)); + ++histogram_[whichRBin][whichThetaBin]; + + ++npairs_; + } + } + + void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { + + if (sd1 == sd2) { + return; + } + + Vector3d p1 = sd1->getPos(); + Vector3d p3 = sd3->getPos(); + + Vector3d c = 0.5 * (p1 + p3); + Vector3d r13 = p3 - p1; + + Vector3d r12 = sd2->getPos() - c; + + if (usePeriodicBoundaryConditions_) { + currentSnapshot_->wrapVector(r12); + currentSnapshot_->wrapVector(r13); + } + + RealType distance = r12.length(); + int whichRBin = int(distance / deltaR_); + + if (distance <= len_) { + + RealType cosAngle = evaluateAngle(sd1, sd2, sd3); RealType halfBin = (nAngleBins_ - 1) * 0.5; int whichThetaBin = int(halfBin * (cosAngle + 1.0)); ++histogram_[whichRBin][whichThetaBin]; @@ -127,9 +259,16 @@ namespace OpenMD { if (rdfStream.is_open()) { rdfStream << "#radial distribution function\n"; rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; - rdfStream << "selection2: (" << selectionScript2_ << ")\n"; - rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; - rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; + rdfStream << "selection2: (" << selectionScript2_ << ")"; + if (doSele3_) { + rdfStream << "\tselection3: (" << selectionScript3_ << ")\n"; + } else { + rdfStream << "\n"; + } + rdfStream << "#nRBins = " << nRBins_ << "\tmaxLen = " + << len_ << "\tdeltaR = " << deltaR_ <<"\n"; + rdfStream << "#nAngleBins =" << nAngleBins_ << "\tdeltaCosAngle = " + << deltaCosAngle_ << "\n"; for (unsigned int i = 0; i < avgGofr_.size(); ++i) { // RealType r = deltaR_ * (i + 0.5); @@ -142,7 +281,8 @@ namespace OpenMD { } } else { - sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str()); + sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", + outputFilename_.c_str()); painCave.isFatal = 1; simError(); } @@ -162,6 +302,14 @@ namespace OpenMD { Vector3d vec; + if (!sd1->isDirectional()) { + sprintf(painCave.errMsg, + "GofRTheta: attempted to use a non-directional object: %s\n", + sd1->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + if (sd1->isAtom()) { AtomType* atype1 = static_cast(sd1)->getAtomType(); MultipoleAdapter ma1 = MultipoleAdapter(atype1); @@ -179,9 +327,38 @@ namespace OpenMD { return dot(r12, vec); } + RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { + Vector3d p1 = sd1->getPos(); + Vector3d p3 = sd3->getPos(); + + Vector3d c = 0.5 * (p1 + p3); + Vector3d r13 = p3 - p1; + + Vector3d r12 = sd2->getPos() - c; + + if (usePeriodicBoundaryConditions_) { + currentSnapshot_->wrapVector(r12); + currentSnapshot_->wrapVector(r13); + } + + r12.normalize(); + r13.normalize(); + + return dot(r12, r13); + } + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { Vector3d v1, v2; + if (!sd1->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega: attempted to use a non-directional object: %s\n", + sd1->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + if (sd1->isAtom()){ AtomType* atype1 = static_cast(sd1)->getAtomType(); MultipoleAdapter ma1 = MultipoleAdapter(atype1); @@ -193,6 +370,14 @@ namespace OpenMD { v1 = sd1->getA().transpose() * V3Z; } + if (!sd2->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + if (sd2->isAtom()) { AtomType* atype2 = static_cast(sd2)->getAtomType(); MultipoleAdapter ma2 = MultipoleAdapter(atype2); @@ -210,7 +395,40 @@ namespace OpenMD { return dot(v1, v2); } + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { + Vector3d v1; + Vector3d v2; + + v1 = sd3->getPos() - sd1->getPos(); + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(v1); + + if (!sd2->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega: attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + if (sd2->isAtom()) { + AtomType* atype2 = static_cast(sd2)->getAtomType(); + MultipoleAdapter ma2 = MultipoleAdapter(atype2); + + if (ma2.isDipole() ) + v2 = sd2->getDipole(); + else + v2 = sd2->getA().transpose() * V3Z; + } else { + v2 = sd2->getA().transpose() * V3Z; + } + + v1.normalize(); + v2.normalize(); + return dot(v1, v2); + } }