45 |
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* Phys Rev B, 28,784,1983 |
46 |
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* |
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*/ |
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48 |
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49 |
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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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namespace oopse { |
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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), evaluator1_(info), |
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seleMan1_(info){ |
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele, |
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double rCut, int lNumber, int nbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info){ |
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|
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setOutputName(getPrefix(filename) + ".obo"); |
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"--sele1 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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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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/* Set up cutoff radius and type of order parameter we are calcuating*/ |
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// Set up cutoff radius and order of the Legendre Polynomial: |
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|
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lNumber_ = lNumber; |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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mSize_ = 2*lNumber_+1; |
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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 = 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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for (sd2 = seleMan1_.beginSelected(j),sd2 |
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sdPairs_.push_back(std::make_pair(sd1, sd2)); |
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} |
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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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delta_Q = 1.0 / nbins; |
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delta_W = 2.0 / nbins; |
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|
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void BondOrderParameter::process |
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() { |
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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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RealType QSq_l; |
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int nBonds; |
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int m, m_index; |
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RealSphericalHarmonic sphericalHarmonic; |
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Q_histogram_.resize(nbins); |
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W_histogram_.resize(nbins); |
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} |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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void BondOrderParameter::initalizeHistogram() { |
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std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
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std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
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} |
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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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void BondOrderParameter::process() { |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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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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std::map<int, RealType> QBar_lm; |
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RealType QSq_l; |
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RealType Q_l; |
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int nBonds; |
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RealSphericalHarmonic sphericalHarmonic; |
112 |
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int i, j; |
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|
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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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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119 |
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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 |
121 |
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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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} |
119 |
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for (int istep = 0; istep < nFrames; istep += step_) { |
120 |
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reader.readFrame(istep); |
121 |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
122 |
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|
123 |
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if (evaluator_.isDynamic()) { |
124 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
125 |
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} |
126 |
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} |
127 |
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// update the positions of atoms which belong to the rigidbodies |
128 |
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129 |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
130 |
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mol = info_->nextMolecule(mi)) { |
131 |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
135 |
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} |
136 |
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|
137 |
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// outer loop is over the selected StuntDoubles: |
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/* Setup QBar */ |
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QBar_lm = new double[mSize_]; |
139 |
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
140 |
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sd = seleMan_.nextSelected(i)) { |
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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) { |
140 |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
141 |
< |
currentSnapshot_->wrapVector(vec); |
142 |
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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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// For this central atom, zero out nBonds and QBar_lm |
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/* Check to see if neighbor is in bond cuttoff*/ |
145 |
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if (r<rCut_){ |
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theta = atan(vec.y()/vec.x()); |
147 |
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phi = acos(vec.z()/r); |
148 |
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for(int m_index = 0; m_index < mSize_; m_index++){ |
149 |
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sphericalHarmonic.setM(m_index-lNumber_); |
150 |
< |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
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} |
152 |
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nBonds++; |
153 |
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} |
154 |
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} |
144 |
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nBonds = 0; |
145 |
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|
146 |
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for (int m = -lNumber_; m <= lNumber_; m++) { |
147 |
> |
QBar_lm[m] = 0.0; |
148 |
> |
} |
149 |
> |
|
150 |
> |
// inner loop is over all other atoms in the system: |
151 |
> |
|
152 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
153 |
> |
mol = info_->nextMolecule(mi)) { |
154 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
155 |
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atom = mol->nextAtom(ai)) { |
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|
158 |
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/*Normalize Qbar by number of Bonds*/ |
159 |
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for ( int m_index = 0;m_index < mSize_; m_index++){ |
160 |
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QBar_lm(m_index) = QBar_lm(m_index)/nBonds; |
161 |
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} |
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< |
|
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} |
160 |
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|
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/*Normalize by number of frames*/ |
162 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
163 |
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QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
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< |
} |
158 |
> |
Vector3d vec = sd->getPos() - atom->getPos(); |
159 |
> |
currentSnapshot_->wrapVector(vec); |
160 |
> |
|
161 |
> |
// Calculate "bonds" and build Q_lm(r) where |
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> |
// Q_lm = Y_lm(theta(r),phi(r)) |
163 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
164 |
> |
// system, we choose standard spherical coordinates |
165 |
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|
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> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
167 |
> |
|
168 |
> |
// Check to see if neighbor is in bond cutoff |
169 |
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|
170 |
> |
if (r < rCut_) { |
171 |
> |
theta = atan2(vec.y(), vec.x()); |
172 |
> |
phi = acos(vec.z()/r); |
173 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
174 |
> |
sphericalHarmonic.setM(m); |
175 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
176 |
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} |
177 |
> |
nBonds++; |
178 |
> |
} |
179 |
> |
} |
180 |
> |
} |
181 |
> |
|
182 |
> |
// Normalize Qbar |
183 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
184 |
> |
QBar_lm[m] /= nBonds; |
185 |
> |
} |
186 |
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|
187 |
+ |
// Find second order invariant Q_l |
188 |
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189 |
+ |
QSq_l = 0.0; |
190 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++){ |
191 |
+ |
QSq_l += pow(QBar_lm[m], 2); |
192 |
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} |
193 |
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Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
194 |
+ |
|
195 |
+ |
// Find Third Order Invariant W_l |
196 |
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|
197 |
< |
/* Find second order invariant Q_l*/ |
197 |
> |
// Make arrays for Wigner3jm |
198 |
> |
double* THRCOF = new double[mSize_]; |
199 |
> |
// Variables for Wigner routine |
200 |
> |
double l_ = (double)lNumber_; |
201 |
> |
double m2Min, m2Max; |
202 |
> |
int error, m1, m2, m3; |
203 |
> |
|
204 |
> |
W_l_ = 0.0; |
205 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
206 |
> |
// Zero work array |
207 |
> |
for (int ii = 0; ii < mSize_; ii+){ |
208 |
> |
THRCOF[i] = 0.0; |
209 |
> |
} |
210 |
> |
// Get Wigner coefficients |
211 |
> |
Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
212 |
> |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
213 |
> |
m2 = floor(m2Min) + m_index - 1; |
214 |
> |
m3 = -m1-m2; |
215 |
> |
W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
216 |
> |
} |
217 |
> |
} |
218 |
|
|
219 |
< |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
176 |
< |
QSq_l += pow(QBar_lm(m),2); |
177 |
< |
} |
178 |
< |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
219 |
> |
W_l_hat = W_l_ / pow(QSq_l, 1.5); |
220 |
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|
221 |
< |
/* Find Third Order Invariant W_l*/ |
221 |
> |
// accumulate histogram data for Q_l and W_l_hat: |
222 |
|
|
223 |
< |
/* Make arrays for Wigner3jm */ |
224 |
< |
double* THRCOF = new double[mSize_]; |
184 |
< |
/* Variables for Wigner routine */ |
185 |
< |
double l_ = (double)lNumber_; |
186 |
< |
double m2Min; |
187 |
< |
double m2Max; |
188 |
< |
int error; |
189 |
< |
int m1; |
190 |
< |
int m2; |
191 |
< |
int m3; |
192 |
< |
|
193 |
< |
for (int m1 = -lNumber_;m <= lNumber_;m1++){ |
194 |
< |
/* Zero work array */ |
195 |
< |
for (i=0; i<mSize_;i++){ |
196 |
< |
THRCOF[i] = 0.0; |
197 |
< |
} |
198 |
< |
/* Get wigner coefficients */ |
199 |
< |
Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error); |
200 |
< |
for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){ |
201 |
< |
m2 = floor(m2Min) + m_index - 1; |
202 |
< |
m3 = -m1-m2; |
203 |
< |
W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_); |
204 |
< |
} |
223 |
> |
collectHistogram(Q_l, W_l_hat); |
224 |
> |
|
225 |
|
} |
226 |
+ |
} |
227 |
+ |
|
228 |
+ |
// Normalize by number of frames |
229 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++){ |
230 |
+ |
QBar_lm[m] /= nFrames; |
231 |
+ |
} |
232 |
+ |
|
233 |
+ |
|
234 |
+ |
|
235 |
+ |
|
236 |
+ |
|
237 |
+ |
writeOrderParameter(); |
238 |
+ |
|
239 |
+ |
} |
240 |
|
|
241 |
+ |
|
242 |
+ |
void BondOrderParameter::processHistogram() { |
243 |
+ |
|
244 |
+ |
int nPairs = getNPairs(); |
245 |
+ |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
246 |
+ |
RealType pairDensity = nPairs /volume * 2.0; |
247 |
+ |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
248 |
|
|
249 |
< |
writeOrderParameter(); |
249 |
> |
for(int i = 0 ; i < histogram_.size(); ++i){ |
250 |
|
|
251 |
+ |
RealType rLower = i * deltaR_; |
252 |
+ |
RealType rUpper = rLower + deltaR_; |
253 |
+ |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
254 |
+ |
RealType nIdeal = volSlice * pairConstant; |
255 |
+ |
|
256 |
+ |
avgGofr_[i] += histogram_[i] / nIdeal; |
257 |
|
} |
258 |
|
|
259 |
+ |
} |
260 |
|
|
261 |
< |
void BondOrderParameter::writeOrderParameter() { |
261 |
> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
262 |
|
|
263 |
< |
std::ofstream os(getOutputFileName().c_str()); |
264 |
< |
os << "#radial distribution function\n"; |
265 |
< |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
266 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
267 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
263 |
> |
if (Q_l < Max_Q) { |
264 |
> |
int whichBin = Q_l / deltaQ_; |
265 |
> |
Q_histogram_[whichBin] += 1; |
266 |
> |
} |
267 |
> |
if (W_l_hat < Max_W) { |
268 |
> |
int whichBin = W_l_hat / deltaW_; |
269 |
> |
W_histogram_[whichBin] += 1; |
270 |
> |
} |
271 |
> |
} |
272 |
> |
|
273 |
|
|
274 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
222 |
< |
os << orderParams_[i].p2 << "\t" |
223 |
< |
<< orderParams_[i].director[0] << "\t" |
224 |
< |
<< orderParams_[i].director[1] << "\t" |
225 |
< |
<< orderParams_[i].director[2] << "\t" |
226 |
< |
<< orderParams_[i].angle << "\n"; |
274 |
> |
void BondOrderParameter::writeOrderParameter() { |
275 |
|
|
276 |
< |
} |
276 |
> |
std::ofstream os(getOutputFileName().c_str()); |
277 |
> |
os << "#Bond Order Parameter\n"; |
278 |
> |
os << "#selection: (" << selectionScript_ << ")\n"; |
279 |
|
|
280 |
< |
} |
280 |
> |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
281 |
> |
os << orderParams_[i].p2 << "\t" |
282 |
> |
<< orderParams_[i].director[0] << "\t" |
283 |
> |
<< orderParams_[i].director[1] << "\t" |
284 |
> |
<< orderParams_[i].director[2] << "\t" |
285 |
> |
<< orderParams_[i].angle << "\n"; |
286 |
|
|
287 |
+ |
} |
288 |
|
} |
289 |
|
|
290 |
+ |
|
291 |
+ |
|
292 |
+ |
} |