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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1041 by gezelter, Wed Sep 20 20:13:40 2006 UTC vs.
Revision 1054 by gezelter, Tue Sep 26 16:08:44 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 1.18 2006-09-26 16:08:44 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/RealSphericalHarmonic.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() {
149      Molecule* mol;
150      Atom* atom;
151      RigidBody* rb;
152 +    int myIndex;
153      SimInfo::MoleculeIterator mi;
154      Molecule::RigidBodyIterator rbIter;
155      Molecule::AtomIterator ai;
156      StuntDouble* sd;
157 <    RealType theta;
157 >    Vector3d vec;
158 >    RealType costheta;
159      RealType phi;
160      RealType r;
161      RealType dist;
162 <    std::map<int, RealType> QBar_lm;
163 <    RealType QSq_l;
164 <    RealType Q_l;
165 <    int nBonds;
166 <    RealSphericalHarmonic sphericalHarmonic;
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;
121 –  
122 –    // Set the l for the spherical harmonic, it doesn't change
123 –    sphericalHarmonic.setL(lNumber_);
175  
125 –
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 +
190      for (int istep = 0; istep < nFrames; istep += step_) {
191        reader.readFrame(istep);
192        frameCounter_++;
# Line 144 | Line 204 | namespace oopse {
204               rb = mol->nextRigidBody(rbIter)) {
205            rb->updateAtoms();
206          }        
207 <      }      
208 <      
207 >      }          
208 >            
209        // outer loop is over the selected StuntDoubles:
210  
211        for (sd = seleMan_.beginSelected(i); sd != NULL;
212             sd = seleMan_.nextSelected(i)) {
213  
214 <        // For this central atom, zero out nBonds and QBar_lm
155 <
214 >        myIndex = sd->getGlobalIndex();
215          nBonds = 0;
216 <      
217 <        for (int m = -lNumber_; m <= lNumber_; m++) {
218 <          QBar_lm[m] = 0.0;
216 >        
217 >        for (int l = 0; l <= lMax_; l++) {
218 >          for (int m = -l; m <= l; m++) {
219 >            q[std::make_pair(l,m)] = 0.0;
220 >          }
221          }
222          
223          // inner loop is over all other atoms in the system:
# Line 166 | Line 227 | namespace oopse {
227            for (atom = mol->beginAtom(ai); atom != NULL;
228                 atom = mol->nextAtom(ai)) {
229  
230 +            if (atom->getGlobalIndex() != myIndex) {
231  
232 <            Vector3d vec = sd->getPos() - atom->getPos();      
233 <            currentSnapshot_->wrapVector(vec);
234 <            
235 <            // Calculate "bonds" and build Q_lm(r) where
236 <            //      Q_lm = Y_lm(theta(r),phi(r))                
237 <            // The spherical harmonics are wrt any arbitrary coordinate
238 <            // system, we choose standard spherical coordinates
239 <            
240 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
241 <            
242 <            // Check to see if neighbor is in bond cutoff
243 <            
244 <            if (r < rCut_) {            
245 <              theta = atan2(vec.y(), vec.x());
246 <              phi = acos(vec.z()/r);
247 <              for(int m = -lNumber_; m <= lNumber_; m++){
248 <                sphericalHarmonic.setM(m);
249 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
250 <              }
251 <              nBonds++;
252 <            }  
232 >              vec = sd->getPos() - atom->getPos();      
233 >              currentSnapshot_->wrapVector(vec);
234 >              
235 >              // Calculate "bonds" and build Q_lm(r) where
236 >              //      Q_lm = Y_lm(theta(r),phi(r))                
237 >              // The spherical harmonics are wrt any arbitrary coordinate
238 >              // system, we choose standard spherical coordinates
239 >              
240 >              r = vec.length();
241 >              
242 >              // Check to see if neighbor is in bond cutoff
243 >              
244 >              if (r < rCut_) {
245 >                costheta = vec.z() / r;
246 >                phi = atan2(vec.y(), vec.x());
247 >
248 >                for (int l = 0; l <= lMax_; l++) {
249 >                  sphericalHarmonic.setL(l);
250 >                  for(int m = -l; m <= l; m++){
251 >                    sphericalHarmonic.setM(m);
252 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
253 >                  }
254 >                }
255 >                nBonds++;
256 >              }  
257 >            }
258            }
259          }
260          
261 <        // Normalize Qbar
262 <        for (int m = -lNumber_;m <= lNumber_; m++){
263 <          QBar_lm[m] /= nBonds;
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
272 <
273 <        QSq_l = 0.0;
274 <        for (int m = -lNumber_; m <= lNumber_; m++){
275 <          QSq_l += pow(QBar_lm[m], 2);  
272 >        
273 >        for (int l = 0; l <= lMax_; l++) {
274 >          q2[l] = 0.0;
275 >          for (int m = -l; m <= l; m++){
276 >            q2[l] += norm(q[std::make_pair(l,m)]);
277 >          }
278 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
279 >                        (RealType)(2*l + 1))/(RealType)nBonds;
280          }
281 <        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
206 <    
281 >
282          // Find Third Order Invariant W_l
283 <
284 <        // Make arrays for Wigner3jm
285 <        double* THRCOF = new double[mSize_];
286 <        // Variables for Wigner routine
287 <        double l_ = (double)lNumber_;
288 <        double m1Pass, m2Min, m2Max;
289 <        int error, m1, m2, m3;
290 <
291 <        RealType W_l;
292 <        RealType W_l_hat;
293 <        W_l = 0.0;
219 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
220 <          // Zero work array
221 <          for (int ii = 0; ii < mSize_; ii++){
222 <            THRCOF[i] = 0.0;
283 >    
284 >        for (int l = 0; l <= lMax_; l++) {
285 >          w[l] = 0.0;
286 >          for (int m1 = -l; m1 <= l; m1++) {
287 >            std::pair<int,int> lm = std::make_pair(l, m1);
288 >            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
289 >              int m2 = m2Min[lm] + mmm;
290 >              int m3 = -m1-m2;
291 >              w[l] += w3j[lm][mmm] * q[lm] *
292 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
293 >            }
294            }
295 <          // Get Wigner coefficients
296 <          m1Pass = (double)m1;
226 <          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
227 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
228 <            m2 = floor(m2Min) + m_index - 1;
229 <            m3 = -m1-m2;
230 <            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
231 <          }
295 >          
296 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
297          }
298  
299 <        W_l_hat = W_l / pow(QSq_l, 1.5);
300 <
301 <        // accumulate histogram data for Q_l and W_l_hat:
302 <
303 <        collectHistogram(Q_l, W_l_hat);
304 <                
299 >        collectHistogram(q_l, w_hat);
300 >        
301 >        Nbonds += nBonds;
302 >        for (int l = 0; l <= lMax_;  l++) {
303 >          for (int m = -l; m <= l; m++) {
304 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
305 >          }
306 >        }
307        }
308      }
309 +      
310 +    // Normalize Qbar2
311 +    for (int l = 0; l <= lMax_; l++) {
312 +      for (int m = -l; m <= l; m++){
313 +        QBar[std::make_pair(l,m)] /= Nbonds;
314 +      }
315 +    }
316      
317 <    writeOrderParameter();
317 >    // Find second order invariant Q_l
318      
319 +    for (int l = 0; l <= lMax_; l++) {
320 +      Q2[l] = 0.0;
321 +      for (int m = -l; m <= l; m++){
322 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
323 +      }
324 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
325 +    }
326 +    
327 +    // Find Third Order Invariant W_l
328 +    
329 +    for (int l = 0; l <= lMax_; l++) {
330 +      W[l] = 0.0;
331 +      for (int m1 = -l; m1 <= l; m1++) {
332 +        std::pair<int,int> lm = std::make_pair(l, m1);
333 +        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
334 +          int m2 = m2Min[lm] + mmm;
335 +          int m3 = -m1-m2;
336 +          W[l] += w3j[lm][mmm] * QBar[lm] *
337 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
338 +        }
339 +      }
340 +      
341 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
342 +    }
343 +    
344 +    writeOrderParameter(Q, W_hat);    
345    }
346  
347 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
348 +                                            std::vector<ComplexType> what) {
349  
350 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
351 <
352 <    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
353 <      int qbin = (Q_l - MinQ_) / deltaQ_;
354 <      Q_histogram_[qbin] += 1;
355 <      Qcount_++;
356 <      sumQ_ += Q_l;
357 <      sumQ2_ += Q_l * Q_l;
358 <    } else {
359 <      sprintf( painCave.errMsg,
360 <               "Q_l value outside reasonable range\n");
361 <      painCave.severity = OOPSE_ERROR;
260 <      painCave.isFatal = 1;
261 <      simError();  
350 >    for (int l = 0; l <= lMax_; l++) {
351 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
352 >        int qbin = (q[l] - MinQ_) / deltaQ_;
353 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
354 >        Qcount_[l]++;      
355 >      } else {
356 >        sprintf( painCave.errMsg,
357 >                 "q_l value outside reasonable range\n");
358 >        painCave.severity = OOPSE_ERROR;
359 >        painCave.isFatal = 1;
360 >        simError();  
361 >      }
362      }
363  
364 <    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
365 <      int wbin = (W_l_hat - MinW_) / deltaW_;
366 <      W_histogram_[wbin] += 1;
367 <      Wcount_++;
368 <      sumW_  += W_l_hat;
369 <      sumW2_ += W_l_hat*W_l_hat;
370 <    } else {
371 <      sprintf( painCave.errMsg,
372 <               "W_l_hat value outside reasonable range\n");
373 <      painCave.severity = OOPSE_ERROR;
374 <      painCave.isFatal = 1;
375 <      simError();  
364 >    for (int l = 0; l <= lMax_; l++) {
365 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
366 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
367 >        W_histogram_[std::make_pair(wbin,l)] += 1;
368 >        Wcount_[l]++;      
369 >      } else {
370 >        sprintf( painCave.errMsg,
371 >                 "Re[w_hat] value outside reasonable range\n");
372 >        painCave.severity = OOPSE_ERROR;
373 >        painCave.isFatal = 1;
374 >        simError();  
375 >      }
376      }
377 +
378    }  
379  
279 –  void BondOrderParameter::writeOrderParameter() {
380  
381 +  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
382 +                                               std::vector<ComplexType> What) {
383 +    
384      std::ofstream osq((getOutputFileName() + "q").c_str());
385  
386      if (osq.is_open()) {
284 –
285 –      RealType qAvg = sumQ_ / (RealType) Qcount_;
286 –      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
387        
388 <      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
388 >      osq << "# Bond Order Parameters\n";
389        osq << "# selection: (" << selectionScript_ << ")\n";
390 <      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
391 <      osq << "# std. dev.: " << qStdDev << "\n";
392 <      
390 >      osq << "# \n";
391 >      for (int l = 0; l <= lMax_; l++) {
392 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
393 >      }
394        // Normalize by number of frames and write it out:
395 <      for (int i = 0; i < Q_histogram_.size(); ++i) {
396 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
397 <        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
395 >      for (int i = 0; i < nBins_; ++i) {
396 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
397 >        osq << Qval;
398 >        for (int l = 0; l <= lMax_; l++) {
399 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
400 >            (RealType)Qcount_[l];
401 >        }
402 >        osq << "\n";
403        }
404 <      
404 >
405        osq.close();
406 +
407      } else {
408        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
409                (getOutputFileName() + "q").c_str());
# Line 307 | Line 414 | namespace oopse {
414      std::ofstream osw((getOutputFileName() + "w").c_str());
415  
416      if (osw.is_open()) {
417 <
311 <      RealType wAvg = sumW_ / (RealType) Wcount_;
312 <      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
313 <      
314 <      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
417 >      osw << "# Bond Order Parameters\n";
418        osw << "# selection: (" << selectionScript_ << ")\n";
419 <      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
420 <      osw << "# std. dev.: " << wStdDev << "\n";
421 <      
419 >      osw << "# \n";
420 >      for (int l = 0; l <= lMax_; l++) {
421 >        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
422 >      }
423        // Normalize by number of frames and write it out:
424 <      for (int i = 0; i < W_histogram_.size(); ++i) {
425 <        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
426 <        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
424 >      for (int i = 0; i < nBins_; ++i) {
425 >        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
426 >        osw << Wval;
427 >        for (int l = 0; l <= lMax_; l++) {
428 >          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
429 >            (RealType)Wcount_[l];
430 >        }
431 >        osw << "\n";
432        }
433 <      
433 >
434        osw.close();
435      } else {
436        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
# Line 329 | Line 438 | namespace oopse {
438        painCave.isFatal = 1;
439        simError();  
440      }
441 +      
442    }
443   }

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