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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3022 by gezelter, Tue Sep 26 01:30:32 2006 UTC vs.
Revision 3087 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;
88 –  }
89  
90 +    // Make arrays for Wigner3jm
91 +    double* THRCOF = new double[2*lMax_+1];
92 +    // Variables for Wigner routine
93 +    double lPass, m1Pass, m2m, m2M;
94 +    int error, mSize;
95 +    mSize = 2*lMax_+1;
96 +
97 +    for (int l = 0; l <= lMax_; l++) {
98 +      lPass = (double)l;
99 +      for (int m1 = -l; m1 <= l; m1++) {
100 +        m1Pass = (double)m1;
101 +
102 +        std::pair<int,int> lm = std::make_pair(l, m1);
103 +        
104 +        // Zero work array
105 +        for (int ii = 0; ii < 2*l + 1; ii++){
106 +          THRCOF[ii] = 0.0;
107 +        }
108 +
109 +        // Get Wigner coefficients
110 +        Wigner3jm(&lPass, &lPass, &lPass,
111 +                  &m1Pass, &m2m, &m2M,
112 +                  THRCOF, &mSize, &error);
113 +        
114 +        m2Min[lm] = (int)floor(m2m);
115 +        m2Max[lm] = (int)floor(m2M);
116 +        
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 128 | Line 172 | namespace oopse {
172      int nBonds, Nbonds;
173      SphericalHarmonic sphericalHarmonic;
174      int i, j;
131 –    // Make arrays for Wigner3jm
132 –    double* THRCOF = new double[2*lMax_+1];
133 –    // Variables for Wigner routine
134 –    double lPass, m1Pass, m2Min, m2Max;
135 –    int error, m1, m2, m3, mSize;
136 –    mSize = 2*lMax_+1;
175  
176      DumpReader reader(info_, dumpFilename_);    
177      int nFrames = reader.getNFrames();
# Line 148 | 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 192 | 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 220 | Line 261 | namespace oopse {
261            }
262          }
263          
223 –        
224 –        for (int l = 0; l <= lMax_; l++) {        
225 –          q_l[l] = 0.0;
226 –          for(int m = -l; m <= l; m++) {
227 –            q_l[l] += norm(q[std::make_pair(l,m)]);
228 –          }    
229 –          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
230 –          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231 –        }
232 –
233 –        // 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 /
241 <                        (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;
248 –          lPass = (double)l;
278            for (int m1 = -l; m1 <= l; m1++) {
279 <            // Zero work array
280 <            for (int ii = 0; ii < 2*l + 1; ii++){
281 <              THRCOF[ii] = 0.0;
279 >            std::pair<int,int> lm = std::make_pair(l, m1);
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] *
284 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
285              }
254 –            // Get Wigner coefficients
255 –            m1Pass = (double)m1;
256 –            
257 –            Wigner3jm(&lPass, &lPass, &lPass,
258 –                      &m1Pass, &m2Min, &m2Max,
259 –                      THRCOF, &mSize, &error);
260 –            
261 –            for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
262 –              m2 = (int)floor(m2Min) + mmm;
263 –              m3 = -m1-m2;
264 –              w[l] += THRCOF[mmm] *
265 –                q[std::make_pair(l,m1)] *
266 –                q[std::make_pair(l,m2)] *
267 –                q[std::make_pair(l,m3)];
268 –            }
286            }
287            
288            w_hat[l] = w[l] / pow(q2[l], 1.5);
# Line 276 | 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 303 | Line 320 | namespace oopse {
320      
321      for (int l = 0; l <= lMax_; l++) {
322        W[l] = 0.0;
306 –      lPass = (double)l;
323        for (int m1 = -l; m1 <= l; m1++) {
324 <        // Zero work array
325 <        for (int ii = 0; ii < 2*l + 1; ii++){
326 <          THRCOF[ii] = 0.0;
324 >        std::pair<int,int> lm = std::make_pair(l, m1);
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] *
329 >            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
330          }
312 –        // Get Wigner coefficients
313 –        m1Pass = (double)m1;
314 –        
315 –        Wigner3jm(&lPass, &lPass, &lPass,
316 –                  &m1Pass, &m2Min, &m2Max,
317 –                  THRCOF, &mSize, &error);
318 –        
319 –        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
320 –          m2 = (int)floor(m2Min) + mmm;
321 –          m3 = -m1-m2;
322 –          W[l] += THRCOF[mmm] *
323 –            QBar[std::make_pair(l,m1)] *
324 –            QBar[std::make_pair(l,m2)] *
325 –            QBar[std::make_pair(l,m3)];
326 –        }
331        }
332        
333        W_hat[l] = W[l] / pow(Q2[l], 1.5);
# Line 356 | 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 384 | 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 405 | 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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