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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 1053 by gezelter, Tue Sep 26 14:33:56 2006 UTC vs.
Revision 1100 by gezelter, Wed Dec 20 21:03:11 2006 UTC

# Line 37 | Line 37
37   * arising out of the use of or inability to use software, even if the
38   * University of Notre Dame has been advised of the possibility of
39   * such damages.
40 + *
41 + *  BondOrderParameter.cpp
42 + *  OOPSE-4
43 + *
44 + *  Created by J. Daniel Gezelter on 09/26/06.
45 + *  @author  J. Daniel Gezelter
46 + *  @version $Id: BondOrderParameter.cpp,v 1.22 2006-12-20 21:03:11 gezelter Exp $
47 + *
48   */
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 – */
49  
50   #include "applications/staticProps/BondOrderParameter.hpp"
51   #include "utils/simError.h"
# Line 82 | 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 104 | 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 113 | 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        }
121      }
122 +    delete [] THRCOF;
123 +    THRCOF = NULL;
124    }
125    
126    BondOrderParameter::~BondOrderParameter() {
127      Q_histogram_.clear();
128      W_histogram_.clear();
129 +    for (int l = 0; l <= lMax_; l++) {
130 +      for (int m = -l; m <= l; m++) {
131 +        w3j[std::make_pair(l,m)].clear();
132 +      }
133 +    }
134 +    w3j.clear();
135 +    m2Min.clear();
136 +    m2Max.clear();
137    }
138 <
138 >  
139    void BondOrderParameter::initalizeHistogram() {
140      for (int bin = 0; bin < nBins_; bin++) {
141        for (int l = 0; l <= lMax_; l++) {
# Line 175 | 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 219 | 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 248 | Line 262 | namespace oopse {
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++) {
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 290 | 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 319 | 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 357 | 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 385 | 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)] / (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 406 | 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)] / (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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