| 71 |
|
|
| 72 |
|
lNumber_ = lNumber; |
| 73 |
|
rCut_ = rCut; |
| 74 |
< |
mSize_ = 2*lNumber_+1; |
| 74 |
> |
mSize_ = 2*lNumber_+1; |
| 75 |
> |
|
| 76 |
> |
// Q can take values from 0 to 1 |
| 77 |
> |
|
| 78 |
> |
MinQ_ = 0.0; |
| 79 |
> |
MaxQ_ = 3.0; |
| 80 |
> |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
| 81 |
> |
Q_histogram_.resize(nbins); |
| 82 |
> |
|
| 83 |
> |
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
| 84 |
> |
// use values for MinW_ and MaxW_ that are slightly larger than this: |
| 85 |
> |
|
| 86 |
> |
MinW_ = -0.18; |
| 87 |
> |
MaxW_ = 0.18; |
| 88 |
> |
deltaW_ = (MaxW_ - MinW_) / nbins; |
| 89 |
> |
W_histogram_.resize(nbins); |
| 90 |
> |
|
| 91 |
|
} |
| 92 |
|
|
| 93 |
|
BondOrderParameter::~BondOrderParameter() { |
| 94 |
+ |
Q_histogram_.clear(); |
| 95 |
+ |
W_histogram_.clear(); |
| 96 |
|
} |
| 97 |
|
|
| 98 |
+ |
void BondOrderParameter::initalizeHistogram() { |
| 99 |
+ |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
| 100 |
+ |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
| 101 |
+ |
} |
| 102 |
+ |
|
| 103 |
|
void BondOrderParameter::process() { |
| 104 |
|
Molecule* mol; |
| 105 |
|
Atom* atom; |
| 114 |
|
RealType phi; |
| 115 |
|
RealType r; |
| 116 |
|
RealType dist; |
| 117 |
+ |
std::map<int,ComplexType> q_lm; |
| 118 |
|
std::map<int,ComplexType> QBar_lm; |
| 119 |
|
RealType QSq_l; |
| 120 |
|
RealType Q_l; |
| 121 |
|
ComplexType W_l; |
| 122 |
|
ComplexType W_l_hat; |
| 123 |
< |
int nBonds; |
| 123 |
> |
int nBonds, Nbonds; |
| 124 |
|
SphericalHarmonic sphericalHarmonic; |
| 125 |
|
int i, j; |
| 126 |
|
// Make arrays for Wigner3jm |
| 154 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 155 |
|
rb->updateAtoms(); |
| 156 |
|
} |
| 157 |
< |
} |
| 158 |
< |
|
| 135 |
< |
nBonds = 0; |
| 136 |
< |
|
| 137 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 138 |
< |
QBar_lm[m] = 0.0; |
| 139 |
< |
} |
| 140 |
< |
|
| 157 |
> |
} |
| 158 |
> |
|
| 159 |
|
// outer loop is over the selected StuntDoubles: |
| 160 |
|
|
| 161 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 162 |
|
sd = seleMan_.nextSelected(i)) { |
| 163 |
|
|
| 164 |
|
myIndex = sd->getGlobalIndex(); |
| 165 |
+ |
nBonds = 0; |
| 166 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 167 |
+ |
q_lm[m] = 0.0; |
| 168 |
+ |
} |
| 169 |
|
|
| 170 |
|
// inner loop is over all other atoms in the system: |
| 171 |
|
|
| 194 |
|
|
| 195 |
|
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 196 |
|
sphericalHarmonic.setM(m); |
| 197 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 197 |
> |
q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 198 |
|
} |
| 199 |
|
nBonds++; |
| 200 |
|
} |
| 201 |
|
} |
| 202 |
|
} |
| 203 |
|
} |
| 204 |
< |
} |
| 204 |
> |
RealType ql = 0.0; |
| 205 |
> |
for(int m=-lNumber_; m<=lNumber_; m++) { |
| 206 |
> |
ql += norm(QBar_lm[m]); |
| 207 |
> |
} |
| 208 |
> |
ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1); |
| 209 |
> |
collectHistogram(sqrt(ql)/(RealType)nBonds); |
| 210 |
> |
|
| 211 |
> |
Nbonds += nBonds; |
| 212 |
> |
for (int m=-lNumber_; m<=lNumber_; m++) { |
| 213 |
> |
QBar_lm[m] += q_lm[m]; |
| 214 |
> |
} |
| 215 |
> |
} |
| 216 |
|
} |
| 217 |
|
|
| 218 |
|
// Normalize Qbar2 |
| 219 |
|
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 220 |
< |
QBar_lm[m] /= nBonds; |
| 220 |
> |
QBar_lm[m] /= Nbonds; |
| 221 |
|
} |
| 222 |
|
|
| 223 |
|
// Find second order invariant Q_l |
| 257 |
|
writeOrderParameter(Q_l, real(W_l_hat)); |
| 258 |
|
} |
| 259 |
|
|
| 260 |
+ |
void BondOrderParameter::collectHistogram(RealType q_l) { |
| 261 |
|
|
| 262 |
+ |
if (q_l >= MinQ_ && q_l < MaxQ_) { |
| 263 |
+ |
int qbin = (q_l - MinQ_) / deltaQ_; |
| 264 |
+ |
Q_histogram_[qbin] += 1; |
| 265 |
+ |
Qcount_++; |
| 266 |
+ |
sumQ_ += q_l; |
| 267 |
+ |
sumQ2_ += q_l * q_l; |
| 268 |
+ |
} else { |
| 269 |
+ |
sprintf( painCave.errMsg, |
| 270 |
+ |
"q_l value outside reasonable range\n"); |
| 271 |
+ |
painCave.severity = OOPSE_ERROR; |
| 272 |
+ |
painCave.isFatal = 1; |
| 273 |
+ |
simError(); |
| 274 |
+ |
} |
| 275 |
+ |
|
| 276 |
+ |
} |
| 277 |
+ |
|
| 278 |
+ |
|
| 279 |
|
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
| 280 |
|
|
| 281 |
|
std::ofstream os(getOutputFileName().c_str()); |
| 287 |
|
os << "# \n"; |
| 288 |
|
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
| 289 |
|
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
| 290 |
+ |
// Normalize by number of frames and write it out: |
| 291 |
+ |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
| 292 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 293 |
+ |
os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
| 294 |
+ |
} |
| 295 |
+ |
|
| 296 |
|
os.close(); |
| 297 |
|
|
| 298 |
|
} else { |
