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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_) { |
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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(); |
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currentSnapshot_->wrapVector(vec); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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} |
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|
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|
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for (int l = 0; l <= lMax_; l++) { |
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q_l[l] = 0.0; |
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for(int m = -l; m <= l; m++) { |
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q_l[l] += norm(q[std::make_pair(l,m)]); |
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} |
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q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
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q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
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} |
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|
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// Find second order invariant Q_l |
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|
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for (int l = 0; l <= lMax_; l++) { |
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q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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q[std::make_pair(l,m)] /= (RealType)nBonds; |
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q2[l] += norm(q[std::make_pair(l,m)]); |
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} |
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< |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
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< |
(RealType)(2*l + 1))/(RealType)nBonds; |
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> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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} |
273 |
< |
|
273 |
> |
|
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// Find Third Order Invariant W_l |
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|
|
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|
for (int l = 0; l <= lMax_; l++) { |
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|
Nbonds += nBonds; |
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|
for (int l = 0; l <= lMax_; l++) { |
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|
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 |
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} |
299 |
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} |
360 |
|
Wcount_[l]++; |
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|
} 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 |
|
} |