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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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+ |
* |
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+ |
* BondOrderParameter.cpp |
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* OOPSE-4 |
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* |
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* Created by J. Daniel Gezelter on 09/26/06. |
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* @author J. Daniel Gezelter |
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* @version $Id: BondOrderParameter.cpp,v 1.21 2006-11-21 20:44:54 gezelter Exp $ |
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* |
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*/ |
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– |
|
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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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} |
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} |
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} |
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+ |
delete [] THRCOF; |
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+ |
THRCOF = NULL; |
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} |
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|
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BondOrderParameter::~BondOrderParameter() { |
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Q_histogram_.clear(); |
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W_histogram_.clear(); |
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+ |
for (int l = 0; l <= lMax_; l++) { |
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+ |
for (int m = -l; m <= l; m++) { |
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+ |
w3j[std::make_pair(l,m)].clear(); |
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+ |
} |
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} |
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w3j.clear(); |
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+ |
m2Min.clear(); |
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+ |
m2Max.clear(); |
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} |
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< |
|
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> |
|
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void BondOrderParameter::initalizeHistogram() { |
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for (int bin = 0; bin < nBins_; bin++) { |
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for (int l = 0; l <= lMax_; l++) { |
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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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W_hat.resize(lMax_+1); |
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+ |
Nbonds = 0; |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
| 192 |
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reader.readFrame(istep); |
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if (atom->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - atom->getPos(); |
| 234 |
< |
currentSnapshot_->wrapVector(vec); |
| 234 |
> |
|
| 235 |
> |
if (usePeriodicBoundaryConditions_) |
| 236 |
> |
currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
| 239 |
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// Q_lm = Y_lm(theta(r),phi(r)) |
| 262 |
|
} |
| 263 |
|
|
| 264 |
|
|
| 251 |
– |
for (int l = 0; l <= lMax_; l++) { |
| 252 |
– |
q_l[l] = 0.0; |
| 253 |
– |
for(int m = -l; m <= l; m++) { |
| 254 |
– |
q_l[l] += norm(q[std::make_pair(l,m)]); |
| 255 |
– |
} |
| 256 |
– |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
| 257 |
– |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
| 258 |
– |
} |
| 259 |
– |
|
| 260 |
– |
// Find second order invariant Q_l |
| 261 |
– |
|
| 265 |
|
for (int l = 0; l <= lMax_; l++) { |
| 266 |
|
q2[l] = 0.0; |
| 267 |
|
for (int m = -l; m <= l; m++){ |
| 268 |
+ |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 269 |
|
q2[l] += norm(q[std::make_pair(l,m)]); |
| 270 |
|
} |
| 271 |
< |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
| 268 |
< |
(RealType)(2*l + 1))/(RealType)nBonds; |
| 271 |
> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 272 |
|
} |
| 273 |
< |
|
| 273 |
> |
|
| 274 |
|
// Find Third Order Invariant W_l |
| 275 |
|
|
| 276 |
|
for (int l = 0; l <= lMax_; l++) { |
| 293 |
|
Nbonds += nBonds; |
| 294 |
|
for (int l = 0; l <= lMax_; l++) { |
| 295 |
|
for (int m = -l; m <= l; m++) { |
| 296 |
< |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
| 296 |
> |
QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
| 297 |
|
} |
| 298 |
|
} |
| 299 |
|
} |
| 360 |
|
Wcount_[l]++; |
| 361 |
|
} else { |
| 362 |
|
sprintf( painCave.errMsg, |
| 363 |
< |
"Re[w_hat] value outside reasonable range\n"); |
| 363 |
> |
"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
| 364 |
|
painCave.severity = OOPSE_ERROR; |
| 365 |
|
painCave.isFatal = 1; |
| 366 |
|
simError(); |
| 388 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 389 |
|
osq << Qval; |
| 390 |
|
for (int l = 0; l <= lMax_; l++) { |
| 391 |
< |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
| 391 |
> |
|
| 392 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
| 393 |
|
} |
| 394 |
|
osq << "\n"; |
| 395 |
|
} |
| 410 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 411 |
|
osw << "# \n"; |
| 412 |
|
for (int l = 0; l <= lMax_; l++) { |
| 413 |
< |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
| 413 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 414 |
|
} |
| 415 |
|
// Normalize by number of frames and write it out: |
| 416 |
|
for (int i = 0; i < nBins_; ++i) { |
| 417 |
|
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 418 |
|
osw << Wval; |
| 419 |
|
for (int l = 0; l <= lMax_; l++) { |
| 420 |
< |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l]; |
| 420 |
> |
|
| 421 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 422 |
|
} |
| 423 |
|
osw << "\n"; |
| 424 |
|
} |
