| 45 |
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* Phys Rev B, 28,784,1983 |
| 46 |
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* |
| 47 |
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*/ |
| 48 |
< |
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| 48 |
> |
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| 49 |
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#include "applications/staticProps/BondOrderParameter.hpp" |
| 50 |
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#include "utils/simError.h" |
| 51 |
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#include "io/DumpReader.hpp" |
| 52 |
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#include "primitives/Molecule.hpp" |
| 53 |
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#include "utils/NumericConstant.hpp" |
| 54 |
< |
#include "math/RealSphericalHarmonic.hpp" |
| 54 |
> |
#include "math/SphericalHarmonic.hpp" |
| 55 |
> |
|
| 56 |
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namespace oopse { |
| 57 |
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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) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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|
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setOutputName(getPrefix(filename) + ".bo"); |
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|
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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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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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|
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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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|
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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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|
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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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> |
BondOrderParameter::~BondOrderParameter() { |
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> |
} |
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|
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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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int myIndex; |
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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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Vector3d vec; |
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RealType costheta; |
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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,ComplexType> QBar_lm; |
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RealType QSq_l; |
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RealType Q_l; |
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ComplexType W_l; |
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ComplexType W_l_hat; |
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int nBonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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// Make arrays for Wigner3jm |
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double* THRCOF = new double[mSize_]; |
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// Variables for Wigner routine |
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double l_ = (double)lNumber_; |
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double m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3; |
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|
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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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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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> |
DumpReader reader(info_, dumpFilename_); |
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> |
int nFrames = reader.getNFrames(); |
| 114 |
> |
frameCounter_ = 0; |
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|
| 116 |
+ |
for (int istep = 0; istep < nFrames; istep += step_) { |
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+ |
reader.readFrame(istep); |
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frameCounter_++; |
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+ |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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+ |
|
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if (evaluator_.isDynamic()) { |
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+ |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
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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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> |
// update the positions of atoms which belong to the rigidbodies |
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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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< |
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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|
| 135 |
< |
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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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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|
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} |
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|
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|
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< |
/* Setup QBar */ |
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QBar_lm = new double[mSize_]; |
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< |
|
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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 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 141 |
< |
currentSnapshot_->wrapVector(vec); |
| 142 |
< |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
| 143 |
< |
* we choose standard spherical coordinates */ |
| 144 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 145 |
< |
|
| 146 |
< |
/* Check to see if neighbor is in bond cuttoff*/ |
| 147 |
< |
if (r<rCut_){ |
| 148 |
< |
theta = atan(vec.y()/vec.x()); |
| 149 |
< |
phi = acos(vec.z()/r); |
| 150 |
< |
for(int m_index = 0; m_index < mSize_; m_index++){ |
| 151 |
< |
sphericalHarmonic.setM(m_index-lNumber_); |
| 152 |
< |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
| 153 |
< |
} |
| 154 |
< |
nBonds++; |
| 155 |
< |
} |
| 156 |
< |
} |
| 157 |
< |
|
| 158 |
< |
/*Normalize Qbar by number of Bonds*/ |
| 159 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 160 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nBonds; |
| 161 |
< |
} |
| 162 |
< |
|
| 163 |
< |
|
| 127 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 128 |
> |
mol = info_->nextMolecule(mi)) { |
| 129 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 130 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 131 |
> |
rb->updateAtoms(); |
| 132 |
> |
} |
| 133 |
> |
} |
| 134 |
> |
|
| 135 |
> |
nBonds = 0; |
| 136 |
> |
|
| 137 |
> |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 138 |
> |
QBar_lm[m] = 0.0; |
| 139 |
|
} |
| 140 |
+ |
|
| 141 |
+ |
// outer loop is over the selected StuntDoubles: |
| 142 |
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|
| 143 |
< |
/*Normalize by number of frames*/ |
| 144 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 168 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
| 169 |
< |
} |
| 143 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 144 |
> |
sd = seleMan_.nextSelected(i)) { |
| 145 |
|
|
| 146 |
+ |
myIndex = sd->getGlobalIndex(); |
| 147 |
+ |
|
| 148 |
+ |
// inner loop is over all other atoms in the system: |
| 149 |
+ |
|
| 150 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 151 |
+ |
mol = info_->nextMolecule(mi)) { |
| 152 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 153 |
+ |
atom = mol->nextAtom(ai)) { |
| 154 |
|
|
| 155 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
| 156 |
|
|
| 157 |
< |
/* Find second order invariant Q_l*/ |
| 157 |
> |
vec = sd->getPos() - atom->getPos(); |
| 158 |
> |
currentSnapshot_->wrapVector(vec); |
| 159 |
> |
|
| 160 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 161 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 162 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 163 |
> |
// system, we choose standard spherical coordinates |
| 164 |
> |
|
| 165 |
> |
r = vec.length(); |
| 166 |
> |
|
| 167 |
> |
// Check to see if neighbor is in bond cutoff |
| 168 |
> |
|
| 169 |
> |
if (r < rCut_) { |
| 170 |
> |
costheta = vec.z() / r; |
| 171 |
> |
phi = atan2(vec.y(), vec.x()); |
| 172 |
> |
|
| 173 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 174 |
> |
sphericalHarmonic.setM(m); |
| 175 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 176 |
> |
} |
| 177 |
> |
nBonds++; |
| 178 |
> |
} |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
> |
} |
| 182 |
> |
} |
| 183 |
> |
} |
| 184 |
|
|
| 185 |
< |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
| 186 |
< |
QSq_l += pow(QBar_lm(m),2); |
| 185 |
> |
// Normalize Qbar2 |
| 186 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 187 |
> |
QBar_lm[m] /= nBonds; |
| 188 |
> |
} |
| 189 |
> |
|
| 190 |
> |
// Find second order invariant Q_l |
| 191 |
> |
|
| 192 |
> |
QSq_l = 0.0; |
| 193 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 194 |
> |
QSq_l += norm(QBar_lm[m]); |
| 195 |
> |
} |
| 196 |
> |
|
| 197 |
> |
std::cout << "qsl = " << QSq_l << "\n"; |
| 198 |
> |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
| 199 |
> |
|
| 200 |
> |
// Find Third Order Invariant W_l |
| 201 |
> |
|
| 202 |
> |
W_l = 0.0; |
| 203 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 204 |
> |
// Zero work array |
| 205 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
| 206 |
> |
THRCOF[ii] = 0.0; |
| 207 |
|
} |
| 208 |
< |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
| 209 |
< |
|
| 210 |
< |
/* Find Third Order Invariant W_l*/ |
| 211 |
< |
|
| 212 |
< |
/* Make arrays for Wigner3jm */ |
| 213 |
< |
double* THRCOF = new double[mSize_]; |
| 214 |
< |
/* Variables for Wigner routine */ |
| 215 |
< |
double l_ = (double)lNumber_; |
| 216 |
< |
double m2Min; |
| 217 |
< |
double m2Max; |
| 218 |
< |
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 |
< |
} |
| 208 |
> |
// Get Wigner coefficients |
| 209 |
> |
m1Pass = (double)m1; |
| 210 |
> |
|
| 211 |
> |
Wigner3jm(&l_, &l_, &l_, |
| 212 |
> |
&m1Pass, &m2Min, &m2Max, |
| 213 |
> |
THRCOF, &mSize_, &error); |
| 214 |
> |
|
| 215 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
| 216 |
> |
m2 = (int)floor(m2Min) + mmm; |
| 217 |
> |
m3 = -m1-m2; |
| 218 |
> |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
| 219 |
|
} |
| 206 |
– |
|
| 207 |
– |
|
| 208 |
– |
writeOrderParameter(); |
| 209 |
– |
|
| 220 |
|
} |
| 221 |
+ |
|
| 222 |
+ |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 223 |
+ |
|
| 224 |
+ |
writeOrderParameter(Q_l, real(W_l_hat)); |
| 225 |
+ |
} |
| 226 |
|
|
| 227 |
|
|
| 228 |
< |
void BondOrderParameter::writeOrderParameter() { |
| 228 |
> |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
| 229 |
|
|
| 230 |
< |
std::ofstream os(getOutputFileName().c_str()); |
| 216 |
< |
os << "#radial distribution function\n"; |
| 217 |
< |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
| 218 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 219 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 230 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 231 |
|
|
| 232 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 233 |
< |
os << orderParams_[i].p2 << "\t" |
| 234 |
< |
<< orderParams_[i].director[0] << "\t" |
| 235 |
< |
<< orderParams_[i].director[1] << "\t" |
| 236 |
< |
<< orderParams_[i].director[2] << "\t" |
| 237 |
< |
<< orderParams_[i].angle << "\n"; |
| 232 |
> |
if (os.is_open()) { |
| 233 |
> |
|
| 234 |
> |
os << "# Bond Order Parameters\n"; |
| 235 |
> |
os << "# selection: (" << selectionScript_ << ")\n"; |
| 236 |
> |
os << "# \n"; |
| 237 |
> |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
| 238 |
> |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
| 239 |
> |
os.close(); |
| 240 |
|
|
| 241 |
< |
} |
| 242 |
< |
|
| 241 |
> |
} else { |
| 242 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 243 |
> |
getOutputFileName().c_str()); |
| 244 |
> |
painCave.isFatal = 1; |
| 245 |
> |
simError(); |
| 246 |
|
} |
| 231 |
– |
|
| 247 |
|
} |
| 248 |
< |
|
| 248 |
> |
} |
