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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3012 by gezelter, Thu Sep 21 18:04:52 2006 UTC vs.
Revision 3079 by gezelter, Tue Nov 21 20:44:54 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 1.21 2006-11-21 20:44:54 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"
52   #include "io/DumpReader.hpp"
53   #include "primitives/Molecule.hpp"
54   #include "utils/NumericConstant.hpp"
54 – #include "math/SphericalHarmonic.hpp"
55  
56   namespace oopse {
57  
58    BondOrderParameter::BondOrderParameter(SimInfo* info,
59                                           const std::string& filename,
60                                           const std::string& sele,
61 <                                         double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62      
63      setOutputName(getPrefix(filename) + ".bo");
64  
# Line 69 | Line 69 | namespace oopse {
69  
70      // Set up cutoff radius and order of the Legendre Polynomial:
71  
72 –    lNumber_ = lNumber;
72      rCut_ = rCut;
73 <    mSize_ = 2*lNumber_+1;    
73 >    nBins_ = nbins;
74 >    Qcount_.resize(lMax_+1);
75 >    Wcount_.resize(lMax_+1);
76  
77      // Q can take values from 0 to 1
78  
79      MinQ_ = 0.0;
80 <    MaxQ_ = 1.0;
80 >    MaxQ_ = 1.1;
81      deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81 –    Q_histogram_.resize(nbins);
82  
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_ = -0.18;
87 <    MaxW_ = 0.18;
86 >    MinW_ = -0.25;
87 >    MaxW_ = 0.25;
88      deltaW_ = (MaxW_ - MinW_) / nbins;
89 –    W_histogram_.resize(nbins);
89  
90 <  }
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 <    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
141 <    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
140 >    for (int bin = 0; bin < nBins_; bin++) {
141 >      for (int l = 0; l <= lMax_; l++) {
142 >        Q_histogram_[std::make_pair(bin,l)] = 0;
143 >        W_histogram_[std::make_pair(bin,l)] = 0;
144 >      }
145 >    }
146    }
147  
148    void BondOrderParameter::process() {
# Line 114 | Line 159 | namespace oopse {
159      RealType phi;
160      RealType r;
161      RealType dist;
162 <    std::map<int, ComplexType> QBar_lm;
163 <    RealType QSq_l;
164 <    RealType Q_l;
165 <    ComplexType W_l;
166 <    ComplexType W_l_hat;
167 <    int nBonds;
162 >    std::map<std::pair<int,int>,ComplexType> q;
163 >    std::vector<RealType> q_l;
164 >    std::vector<RealType> q2;
165 >    std::vector<ComplexType> w;
166 >    std::vector<ComplexType> w_hat;
167 >    std::map<std::pair<int,int>,ComplexType> QBar;
168 >    std::vector<RealType> Q2;
169 >    std::vector<RealType> Q;
170 >    std::vector<ComplexType> W;
171 >    std::vector<ComplexType> W_hat;
172 >    int nBonds, Nbonds;
173      SphericalHarmonic sphericalHarmonic;
174      int i, j;
125 –    // Make arrays for Wigner3jm
126 –    double* THRCOF = new double[mSize_];
127 –    // Variables for Wigner routine
128 –    double l_ = (double)lNumber_;
129 –    double m1Pass, m2Min, m2Max;
130 –    int error, m1, m2, m3;
175  
132 –    // Set the l for the spherical harmonic, it doesn't change
133 –    sphericalHarmonic.setL(lNumber_);
134 –
176      DumpReader reader(info_, dumpFilename_);    
177      int nFrames = reader.getNFrames();
178      frameCounter_ = 0;
179  
180 +    q_l.resize(lMax_+1);
181 +    q2.resize(lMax_+1);
182 +    w.resize(lMax_+1);
183 +    w_hat.resize(lMax_+1);
184 +
185 +    Q2.resize(lMax_+1);
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);
193        frameCounter_++;
# Line 153 | Line 205 | namespace oopse {
205               rb = mol->nextRigidBody(rbIter)) {
206            rb->updateAtoms();
207          }        
208 <      }      
209 <      
208 >      }          
209 >            
210        // outer loop is over the selected StuntDoubles:
211  
212        for (sd = seleMan_.beginSelected(i); sd != NULL;
213             sd = seleMan_.nextSelected(i)) {
214  
215          myIndex = sd->getGlobalIndex();
164 –
165 –        // For this central atom, zero out nBonds and QBar_lm
166 –
216          nBonds = 0;
217 <      
218 <        for (int m = -lNumber_; m <= lNumber_; m++) {
219 <          QBar_lm[m] = 0.0;
217 >        
218 >        for (int l = 0; l <= lMax_; l++) {
219 >          for (int m = -l; m <= l; m++) {
220 >            q[std::make_pair(l,m)] = 0.0;
221 >          }
222          }
223          
224          // inner loop is over all other atoms in the system:
# Line 180 | 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 194 | Line 247 | namespace oopse {
247                if (r < rCut_) {
248                  costheta = vec.z() / r;
249                  phi = atan2(vec.y(), vec.x());
250 <                
251 <                for(int m = -lNumber_; m <= lNumber_; m++){
252 <                  sphericalHarmonic.setM(m);
253 <                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
250 >
251 >                for (int l = 0; l <= lMax_; l++) {
252 >                  sphericalHarmonic.setL(l);
253 >                  for(int m = -l; m <= l; m++){
254 >                    sphericalHarmonic.setM(m);
255 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256 >                  }
257                  }
258                  nBonds++;
259                }  
# Line 205 | Line 261 | namespace oopse {
261            }
262          }
263          
264 <        // Normalize Qbar2
265 <        for (int m = -lNumber_;m <= lNumber_; m++){
266 <          QBar_lm[m] /= nBonds;
267 <          std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
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 / (RealType)(2*l + 1));
272          }
273 <
274 <        // Find second order invariant Q_l
275 <
276 <        QSq_l = 0.0;
277 <        for (int m = -lNumber_; m <= lNumber_; m++){
278 <          QSq_l += norm(QBar_lm[m]);
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++) {
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 >            }
286 >          }
287 >          
288 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
289          }
220 –        std::cout << "qsq_l = " << QSq_l << "\n";
221 –        Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
222 –                   (2.0*(RealType)lNumber_ + 1.0));
290  
291 <        // Find Third Order Invariant W_l
291 >        collectHistogram(q_l, w_hat);
292          
293 <        W_l = 0.0;
294 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
295 <          // Zero work array
296 <          for (int ii = 0; ii < mSize_; ii++){
230 <            THRCOF[i] = 0.0;
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)] += (RealType)nBonds*q[std::make_pair(l,m)];
297            }
232 –          // Get Wigner coefficients
233 –          m1Pass = (double)m1;
234 –          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
235 –          for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
236 –            m2 = floor(m2Min) + m_index - 1;
237 –            m3 = -m1-m2;
238 –            W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3];
239 –          }
298          }
241 –        
242 –        W_l_hat = W_l / pow(QSq_l, 1.5);
243 –        
244 –        // accumulate histogram data for Q_l and W_l_hat:
245 –
246 –        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
247 –        collectHistogram(Q_l, real(W_l_hat));
248 –                
299        }
300      }
301 +      
302 +    // Normalize Qbar2
303 +    for (int l = 0; l <= lMax_; l++) {
304 +      for (int m = -l; m <= l; m++){
305 +        QBar[std::make_pair(l,m)] /= Nbonds;
306 +      }
307 +    }
308      
309 <    writeOrderParameter();
309 >    // Find second order invariant Q_l
310      
311 +    for (int l = 0; l <= lMax_; l++) {
312 +      Q2[l] = 0.0;
313 +      for (int m = -l; m <= l; m++){
314 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
315 +      }
316 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317 +    }
318 +    
319 +    // Find Third Order Invariant W_l
320 +    
321 +    for (int l = 0; l <= lMax_; l++) {
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++) {
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 +        }
331 +      }
332 +      
333 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
334 +    }
335 +    
336 +    writeOrderParameter(Q, W_hat);    
337    }
338  
339 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340 +                                            std::vector<ComplexType> what) {
341  
342 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
343 <
344 <    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
345 <      int qbin = (Q_l - MinQ_) / deltaQ_;
346 <      Q_histogram_[qbin] += 1;
347 <      Qcount_++;
348 <      sumQ_ += Q_l;
349 <      sumQ2_ += Q_l * Q_l;
350 <    } else {
351 <      sprintf( painCave.errMsg,
352 <               "Q_l value outside reasonable range\n");
353 <      painCave.severity = OOPSE_ERROR;
269 <      painCave.isFatal = 1;
270 <      simError();  
342 >    for (int l = 0; l <= lMax_; l++) {
343 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344 >        int qbin = (q[l] - MinQ_) / deltaQ_;
345 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
346 >        Qcount_[l]++;      
347 >      } else {
348 >        sprintf( painCave.errMsg,
349 >                 "q_l value outside reasonable range\n");
350 >        painCave.severity = OOPSE_ERROR;
351 >        painCave.isFatal = 1;
352 >        simError();  
353 >      }
354      }
355  
356 <    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
357 <      int wbin = (W_l_hat - MinW_) / deltaW_;
358 <      W_histogram_[wbin] += 1;
359 <      Wcount_++;
360 <      sumW_  += W_l_hat;
361 <      sumW2_ += W_l_hat*W_l_hat;
362 <    } else {
363 <      sprintf( painCave.errMsg,
364 <               "W_l_hat value outside reasonable range\n");
365 <      painCave.severity = OOPSE_ERROR;
366 <      painCave.isFatal = 1;
367 <      simError();  
356 >    for (int l = 0; l <= lMax_; l++) {
357 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
359 >        W_histogram_[std::make_pair(wbin,l)] += 1;
360 >        Wcount_[l]++;      
361 >      } else {
362 >        sprintf( painCave.errMsg,
363 >                 "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
364 >        painCave.severity = OOPSE_ERROR;
365 >        painCave.isFatal = 1;
366 >        simError();  
367 >      }
368      }
369 +
370    }  
371  
288 –  void BondOrderParameter::writeOrderParameter() {
372  
373 +  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374 +                                               std::vector<ComplexType> What) {
375 +    
376      std::ofstream osq((getOutputFileName() + "q").c_str());
377  
378      if (osq.is_open()) {
293 –
294 –      RealType qAvg = sumQ_ / (RealType) Qcount_;
295 –      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
379        
380 <      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
380 >      osq << "# Bond Order Parameters\n";
381        osq << "# selection: (" << selectionScript_ << ")\n";
382 <      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
383 <      osq << "# std. dev.: " << qStdDev << "\n";
384 <      
382 >      osq << "# \n";
383 >      for (int l = 0; l <= lMax_; l++) {
384 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385 >      }
386        // Normalize by number of frames and write it out:
387 <      for (int i = 0; i < Q_histogram_.size(); ++i) {
388 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
389 <        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
387 >      for (int i = 0; i < nBins_; ++i) {
388 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
389 >        osq << Qval;
390 >        for (int l = 0; l <= lMax_; l++) {
391 >
392 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393 >        }
394 >        osq << "\n";
395        }
396 <      
396 >
397        osq.close();
398 +
399      } else {
400        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401                (getOutputFileName() + "q").c_str());
# Line 316 | Line 406 | namespace oopse {
406      std::ofstream osw((getOutputFileName() + "w").c_str());
407  
408      if (osw.is_open()) {
409 <
320 <      RealType wAvg = sumW_ / (RealType) Wcount_;
321 <      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
322 <      
323 <      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
409 >      osw << "# Bond Order Parameters\n";
410        osw << "# selection: (" << selectionScript_ << ")\n";
411 <      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
412 <      osw << "# std. dev.: " << wStdDev << "\n";
413 <      
411 >      osw << "# \n";
412 >      for (int l = 0; l <= lMax_; l++) {
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 < W_histogram_.size(); ++i) {
417 <        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
418 <        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
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 >
421 >          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422 >        }
423 >        osw << "\n";
424        }
425 <      
425 >
426        osw.close();
427      } else {
428        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
# Line 338 | Line 430 | namespace oopse {
430        painCave.isFatal = 1;
431        simError();  
432      }
433 +      
434    }
435   }

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