| 39 |
|
* such damages. |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
+ |
|
| 43 |
+ |
/* Creates orientational bond order parameters as outlined by |
| 44 |
+ |
* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
| 45 |
+ |
* Phys Rev B, 28,784,1983 |
| 46 |
+ |
* |
| 47 |
+ |
*/ |
| 48 |
+ |
|
| 49 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
| 50 |
|
#include "utils/simError.h" |
| 51 |
|
#include "io/DumpReader.hpp" |
| 52 |
|
#include "primitives/Molecule.hpp" |
| 53 |
|
#include "utils/NumericConstant.hpp" |
| 54 |
+ |
#include "math/RealSphericalHarmonic.hpp" |
| 55 |
|
namespace oopse { |
| 56 |
|
|
| 57 |
|
|
| 61 |
|
selectionScript1_(sele1), evaluator1_(info), |
| 62 |
|
seleMan1_(info){ |
| 63 |
|
|
| 64 |
< |
setOutputName(getPrefix(filename) + ".p2"); |
| 64 |
> |
setOutputName(getPrefix(filename) + ".obo"); |
| 65 |
|
|
| 66 |
|
evaluator1_.loadScriptString(sele1); |
| 67 |
|
evaluator2_.loadScriptString(sele2); |
| 76 |
|
simError(); |
| 77 |
|
} |
| 78 |
|
|
| 79 |
+ |
/* Set up cutoff radius and type of order parameter we are calcuating*/ |
| 80 |
+ |
lNumber_ = lNumber; |
| 81 |
+ |
rCut_ = rCut; |
| 82 |
+ |
mSize_ = 2*lNumber_+1; |
| 83 |
|
|
| 84 |
|
int i; |
| 85 |
|
int j; |
| 100 |
|
RigidBody* rb; |
| 101 |
|
SimInfo::MoleculeIterator mi; |
| 102 |
|
Molecule::RigidBodyIterator rbIter; |
| 103 |
+ |
RealType theta; |
| 104 |
+ |
RealType phi; |
| 105 |
+ |
RealType r; |
| 106 |
+ |
RealType dist; |
| 107 |
+ |
RealType* QBar_lm; |
| 108 |
+ |
int nBonds; |
| 109 |
+ |
RealSphericalHarmonic sphericalHarmonic; |
| 110 |
|
|
| 111 |
+ |
|
| 112 |
|
DumpReader reader(info_, dumpFilename_); |
| 113 |
|
int nFrames = reader.getNFrames(); |
| 114 |
|
|
| 115 |
+ |
/*Set the l for the spherical harmonic, it doesn't change*/ |
| 116 |
+ |
sphericalHarmonic.setL(lNumber_); |
| 117 |
+ |
|
| 118 |
|
for (int i = 0; i < nFrames; i += step_) { |
| 119 |
|
reader.readFrame(i); |
| 120 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 121 |
< |
|
| 121 |
> |
nBonds = 0; |
| 122 |
|
|
| 123 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 124 |
|
//change the positions of atoms which belong to the rigidbodies |
| 128 |
|
|
| 129 |
|
} |
| 130 |
|
|
| 131 |
< |
Mat3x3d orderTensor(0.0); |
| 131 |
> |
/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
| 132 |
|
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 133 |
|
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 134 |
|
currentSnapshot_->wrapVector(vec); |
| 135 |
< |
vec.normalize(); |
| 136 |
< |
orderTensor +=outProduct(vec, vec); |
| 135 |
> |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
| 136 |
> |
* we choose standard spherical coordinates */ |
| 137 |
> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 138 |
> |
|
| 139 |
> |
/* Check to see if neighbor is in bond cuttoff*/ |
| 140 |
> |
if (r<rCut_){ |
| 141 |
> |
theta = atan(vec.y()/vec.x()); |
| 142 |
> |
phi = acos(vec.z()/r); |
| 143 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 144 |
> |
sphericalHarmonic.setM(m); |
| 145 |
> |
QBar_lm(m) += sphericalHarmonic.getValueAt(theta,phi); |
| 146 |
> |
} |
| 147 |
> |
nBonds++; |
| 148 |
> |
} |
| 149 |
|
} |
| 150 |
|
|
| 151 |
< |
orderTensor /= sdPairs_.size(); |
| 152 |
< |
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 151 |
> |
/*Normalize Qbar*/ |
| 152 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 153 |
> |
QBar_lm(m) = QBar_lm(m)/nBonds; |
| 154 |
> |
} |
| 155 |
|
|
| 156 |
< |
Vector3d eigenvalues; |
| 157 |
< |
Mat3x3d eigenvectors; |
| 158 |
< |
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
| 159 |
< |
|
| 160 |
< |
int which; |
| 161 |
< |
RealType maxEval = 0.0; |
| 162 |
< |
for(int k = 0; k< 3; k++){ |
| 163 |
< |
if(fabs(eigenvalues[k]) > maxEval){ |
| 164 |
< |
which = k; |
| 165 |
< |
maxEval = fabs(eigenvalues[k]); |
| 166 |
< |
} |
| 167 |
< |
} |
| 168 |
< |
RealType p2 = 1.5 * maxEval; |
| 169 |
< |
|
| 170 |
< |
//the eigen vector is already normalized in SquareMatrix3::diagonalize |
| 171 |
< |
Vector3d director = eigenvectors.getColumn(which); |
| 172 |
< |
if (director[0] < 0) { |
| 173 |
< |
director.negate(); |
| 174 |
< |
} |
| 156 |
> |
|
| 157 |
> |
} |
| 158 |
> |
|
| 159 |
> |
/*Normalize by number of frames*/ |
| 160 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 161 |
> |
QBar_lm(m) = QBar_lm(m)/nFrames; |
| 162 |
> |
} |
| 163 |
> |
|
| 164 |
> |
|
| 165 |
> |
|
| 166 |
> |
/* Find second order invariant Q_l*/ |
| 167 |
> |
|
| 168 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 169 |
> |
QSq_l += pow(QBar_lm(m),2); |
| 170 |
> |
} |
| 171 |
> |
Q_l = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
| 172 |
> |
|
| 173 |
> |
/* Find Third Order Invariant W_l*/ |
| 174 |
> |
for (int m = -lNumber_;m<= lNumber_;m++){ |
| 175 |
> |
|
| 176 |
> |
|
| 177 |
> |
} |
| 178 |
> |
|
| 179 |
> |
|
| 180 |
> |
writeOrderParameter(); |
| 181 |
> |
|
| 182 |
> |
} |
| 183 |
|
|
| 184 |
< |
RealType angle = 0.0; |
| 185 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 186 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 142 |
< |
currentSnapshot_->wrapVector(vec); |
| 143 |
< |
vec.normalize(); |
| 184 |
> |
void BondOrderParameter::initalizeHistogram() { |
| 185 |
> |
std::fill(histogram_.begin(), histogram_.end(), 0); |
| 186 |
> |
} |
| 187 |
|
|
| 188 |
< |
angle += acos(dot(vec, director)) ; |
| 146 |
< |
} |
| 147 |
< |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 188 |
> |
void BondOrderParameter::processHistogram() { |
| 189 |
|
|
| 190 |
< |
OrderParam param; |
| 191 |
< |
param.p2 = p2; |
| 192 |
< |
param.director = director; |
| 193 |
< |
param.angle = angle; |
| 190 |
> |
int nPairs = getNPairs(); |
| 191 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 192 |
> |
RealType pairDensity = nPairs /volume * 2.0; |
| 193 |
> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 194 |
|
|
| 195 |
< |
orderParams_.push_back(param); |
| 195 |
> |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 196 |
> |
|
| 197 |
> |
RealType rLower = i * deltaR_; |
| 198 |
> |
RealType rUpper = rLower + deltaR_; |
| 199 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 200 |
> |
RealType nIdeal = volSlice * pairConstant; |
| 201 |
> |
|
| 202 |
> |
avgGofr_[i] += histogram_[i] / nIdeal; |
| 203 |
> |
} |
| 204 |
> |
|
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
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; |
| 216 |
+ |
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 |
|
|
| 158 |
– |
writeP2(); |
| 159 |
– |
|
| 160 |
– |
} |
| 226 |
|
|
| 227 |
+ |
|
| 228 |
+ |
|
| 229 |
+ |
|
| 230 |
+ |
|
| 231 |
|
void BondOrderParameter::writeOrderParameter() { |
| 232 |
|
|
| 233 |
|
std::ofstream os(getOutputFileName().c_str()); |
