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root/OpenMD/trunk/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1054 by gezelter, Tue Sep 26 16:08:44 2006 UTC vs.
Revision 1100 by gezelter, Wed Dec 20 21:03:11 2006 UTC

# Line 43 | Line 43
43   *
44   *  Created by J. Daniel Gezelter on 09/26/06.
45   *  @author  J. Daniel Gezelter
46 < *  @version $Id: BondOrderParameter.cpp,v 1.18 2006-09-26 16:08:44 gezelter Exp $
46 > *  @version $Id: BondOrderParameter.cpp,v 1.22 2006-12-20 21:03:11 gezelter Exp $
47   *
48   */
49  
# Line 83 | Line 83 | namespace oopse {
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_ = -0.25;
87 <    MaxW_ = 0.25;
86 >    MinW_ = -1.1;
87 >    MaxW_ = 1.1;
88      deltaW_ = (MaxW_ - MinW_) / nbins;
89  
90      // Make arrays for Wigner3jm
# Line 105 | Line 105 | namespace oopse {
105          for (int ii = 0; ii < 2*l + 1; ii++){
106            THRCOF[ii] = 0.0;
107          }
108 <            
108 >
109          // Get Wigner coefficients
110          Wigner3jm(&lPass, &lPass, &lPass,
111                    &m1Pass, &m2m, &m2M,
# Line 114 | Line 114 | namespace oopse {
114          m2Min[lm] = (int)floor(m2m);
115          m2Max[lm] = (int)floor(m2M);
116          
117 <        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
117 >        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
118            w3j[lm].push_back(THRCOF[mmm]);
119          }
120        }
# Line 186 | Line 186 | namespace oopse {
186      Q.resize(lMax_+1);
187      W.resize(lMax_+1);
188      W_hat.resize(lMax_+1);
189 +    Nbonds = 0;
190  
191      for (int istep = 0; istep < nFrames; istep += step_) {
192        reader.readFrame(istep);
# Line 230 | Line 231 | namespace oopse {
231              if (atom->getGlobalIndex() != myIndex) {
232  
233                vec = sd->getPos() - atom->getPos();      
234 <              currentSnapshot_->wrapVector(vec);
234 >
235 >              if (usePeriodicBoundaryConditions_)
236 >                currentSnapshot_->wrapVector(vec);
237                
238                // Calculate "bonds" and build Q_lm(r) where
239                //      Q_lm = Y_lm(theta(r),phi(r))                
# Line 258 | Line 261 | namespace oopse {
261            }
262          }
263          
261 –        
262 –        for (int l = 0; l <= lMax_; l++) {        
263 –          q_l[l] = 0.0;
264 –          for(int m = -l; m <= l; m++) {
265 –            q_l[l] += norm(q[std::make_pair(l,m)]);
266 –          }    
267 –          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
268 –          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
269 –        }
270 –
271 –        // Find second order invariant Q_l
264          
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 /
279 <                        (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++) {
277            w[l] = 0.0;
278            for (int m1 = -l; m1 <= l; m1++) {
279              std::pair<int,int> lm = std::make_pair(l, m1);
280 <            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
280 >            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
281                int m2 = m2Min[lm] + mmm;
282                int m3 = -m1-m2;
283                w[l] += w3j[lm][mmm] * q[lm] *
# Line 301 | Line 293 | namespace oopse {
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        }
# Line 330 | Line 322 | namespace oopse {
322        W[l] = 0.0;
323        for (int m1 = -l; m1 <= l; m1++) {
324          std::pair<int,int> lm = std::make_pair(l, m1);
325 <        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
325 >        for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
326            int m2 = m2Min[lm] + mmm;
327            int m3 = -m1-m2;
328            W[l] += w3j[lm][mmm] * QBar[lm] *
# Line 368 | Line 360 | namespace oopse {
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();  
# Line 396 | Line 388 | namespace oopse {
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)] /
392 <            (RealType)Qcount_[l];
391 >
392 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393          }
394          osq << "\n";
395        }
# Line 418 | Line 410 | namespace oopse {
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)] /
421 <            (RealType)Wcount_[l];
420 >
421 >          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422          }
423          osw << "\n";
424        }

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