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* such damages. |
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*/ |
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< |
#include "applications/staticProps/P2OrderParameter.hpp" |
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|
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/* Creates orientational bond order parameters as outlined by |
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
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* Phys Rev B, 28,784,1983 |
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* |
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*/ |
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|
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#include "applications/staticProps/BondOrderParameter.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/RealSphericalHarmonic.hpp" |
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namespace oopse { |
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P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double rCut, int lNumber) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info){ |
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selectionScript1_(sele1), evaluator1_(info), |
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seleMan1_(info){ |
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setOutputName(getPrefix(filename) + ".p2"); |
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setOutputName(getPrefix(filename) + ".obo"); |
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|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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simError(); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"--sele2 must be static selection\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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/* Set up cutoff radius and type of order parameter we are calcuating*/ |
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lNumber_ = lNumber; |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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|
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if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
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sprintf( painCave.errMsg, |
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"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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|
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} |
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|
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int i; |
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int j; |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); |
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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j); |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
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} |
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void P2OrderParameter::process() { |
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void BondOrderParameter::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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RealType theta; |
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RealType phi; |
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RealType r; |
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RealType dist; |
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RealType* QBar_lm; |
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int nBonds; |
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RealSphericalHarmonic sphericalHarmonic; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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/*Set the l for the spherical harmonic, it doesn't change*/ |
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sphericalHarmonic.setL(lNumber_); |
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|
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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nBonds = 0; |
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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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} |
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Mat3x3d orderTensor(0.0); |
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/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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orderTensor +=outProduct(vec, vec); |
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/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
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* we choose standard spherical coordinates */ |
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r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
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|
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/* Check to see if neighbor is in bond cuttoff*/ |
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if (r<rCut_){ |
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theta = atan(vec.y()/vec.x()); |
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phi = acos(vec.z()/r); |
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for(int m = -lNumber_; m <= lNumber_; m++){ |
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sphericalHarmonic.setM(m); |
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QBar_lm(m) += sphericalHarmonic.getValueAt(theta,phi); |
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} |
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nBonds++; |
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} |
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} |
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|
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< |
orderTensor /= sdPairs_.size(); |
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orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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/*Normalize Qbar*/ |
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm(m) = QBar_lm(m)/nBonds; |
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} |
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|
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Vector3d eigenvalues; |
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Mat3x3d eigenvectors; |
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Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
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|
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int which; |
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RealType maxEval = 0.0; |
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for(int k = 0; k< 3; k++){ |
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if(fabs(eigenvalues[k]) > maxEval){ |
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which = k; |
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maxEval = fabs(eigenvalues[k]); |
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} |
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} |
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RealType p2 = 1.5 * maxEval; |
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|
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//the eigen vector is already normalized in SquareMatrix3::diagonalize |
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Vector3d director = eigenvectors.getColumn(which); |
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if (director[0] < 0) { |
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director.negate(); |
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} |
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|
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} |
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|
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/*Normalize by number of frames*/ |
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm(m) = QBar_lm(m)/nFrames; |
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} |
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|
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|
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|
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/* Find second order invariant Q_l*/ |
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|
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QSq_l += pow(QBar_lm(m),2); |
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} |
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> |
Q_l = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
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> |
|
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> |
/* Find Third Order Invariant W_l*/ |
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for (int m = -lNumber_;m<= lNumber_;m++){ |
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> |
|
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> |
|
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} |
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> |
|
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> |
|
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> |
writeOrderParameter(); |
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> |
|
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> |
} |
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|
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< |
RealType angle = 0.0; |
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< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
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< |
currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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> |
void BondOrderParameter::initalizeHistogram() { |
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> |
std::fill(histogram_.begin(), histogram_.end(), 0); |
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> |
} |
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|
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< |
angle += acos(dot(vec, director)) ; |
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< |
} |
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< |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
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> |
void BondOrderParameter::processHistogram() { |
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|
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< |
OrderParam param; |
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< |
param.p2 = p2; |
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< |
param.director = director; |
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< |
param.angle = angle; |
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> |
int nPairs = getNPairs(); |
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> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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> |
RealType pairDensity = nPairs /volume * 2.0; |
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> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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|
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< |
orderParams_.push_back(param); |
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> |
for(int i = 0 ; i < histogram_.size(); ++i){ |
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> |
|
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> |
RealType rLower = i * deltaR_; |
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> |
RealType rUpper = rLower + deltaR_; |
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> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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> |
RealType nIdeal = volSlice * pairConstant; |
| 201 |
> |
|
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> |
avgGofr_[i] += histogram_[i] / nIdeal; |
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> |
} |
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> |
|
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> |
} |
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> |
|
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> |
void BondOrderParameter::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 208 |
> |
|
| 209 |
> |
if (sd1 == sd2) { |
| 210 |
> |
return; |
| 211 |
> |
} |
| 212 |
|
|
| 213 |
+ |
Vector3d pos1 = sd1->getPos(); |
| 214 |
+ |
Vector3d pos2 = sd2->getPos(); |
| 215 |
+ |
Vector3d r12 = pos2 - pos1; |
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+ |
currentSnapshot_->wrapVector(r12); |
| 217 |
+ |
|
| 218 |
+ |
RealType distance = r12.length(); |
| 219 |
+ |
|
| 220 |
+ |
if (distance < len_) { |
| 221 |
+ |
int whichBin = distance / deltaR_; |
| 222 |
+ |
histogram_[whichBin] += 2; |
| 223 |
+ |
} |
| 224 |
|
} |
| 225 |
|
|
| 175 |
– |
writeP2(); |
| 176 |
– |
|
| 177 |
– |
} |
| 226 |
|
|
| 179 |
– |
void P2OrderParameter::writeP2() { |
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|
|
| 228 |
+ |
|
| 229 |
+ |
|
| 230 |
+ |
|
| 231 |
+ |
void BondOrderParameter::writeOrderParameter() { |
| 232 |
+ |
|
| 233 |
|
std::ofstream os(getOutputFileName().c_str()); |
| 234 |
|
os << "#radial distribution function\n"; |
| 235 |
|
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
