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root/group/trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3007 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 3054 by gezelter, Wed Oct 18 21:58:48 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 1.19 2006-10-18 21:58:47 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"
55 < #include "math/RealSphericalHarmonic.hpp"
55 >
56   namespace oopse {
57  
57 –
58    BondOrderParameter::BondOrderParameter(SimInfo* info,
59                                           const std::string& filename,
60                                           const std::string& sele,
61 <                                         double rCut, int lNumber, int nbins)
62 <    : StaticAnalyser(info, filename), selectionScript_(sele),
63 <      evaluator_(info), seleMan_(info){
61 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62      
63 <    setOutputName(getPrefix(filename) + ".obo");
63 >    setOutputName(getPrefix(filename) + ".bo");
64  
65      evaluator_.loadScriptString(sele);
66      if (!evaluator_.isDynamic()) {
# Line 71 | Line 69 | namespace oopse {
69  
70      // Set up cutoff radius and order of the Legendre Polynomial:
71  
74 –    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 <    // Set the l for the spherical harmonic, it doesn't change
77 >    // Q can take values from 0 to 1
78  
79 <    sphericalHarmonic.setL(lNumber_);
79 >    MinQ_ = 0.0;
80 >    MaxQ_ = 1.1;
81 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
82  
83 <    delta_Q = 1.0 / nbins;
84 <    delta_W = 2.0 / nbins;
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 <    Q_histogram_.resize(nbins);
87 <    W_histogram_.resize(nbins);
86 >    MinW_ = -0.25;
87 >    MaxW_ = 0.25;
88 >    deltaW_ = (MaxW_ - MinW_) / 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 +  
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;
175 <  
114 <  
175 >
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_++;
193        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
194        
195        if (evaluator_.isDynamic()) {
# Line 132 | 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
143 <
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 154 | 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 >
234 >              if (usePeriodicBoundaryConditions_)
235 >                currentSnapshot_->wrapVector(vec);
236 >              
237 >              // Calculate "bonds" and build Q_lm(r) where
238 >              //      Q_lm = Y_lm(theta(r),phi(r))                
239 >              // The spherical harmonics are wrt any arbitrary coordinate
240 >              // system, we choose standard spherical coordinates
241 >              
242 >              r = vec.length();
243 >              
244 >              // Check to see if neighbor is in bond cutoff
245 >              
246 >              if (r < rCut_) {
247 >                costheta = vec.z() / r;
248 >                phi = atan2(vec.y(), vec.x());
249 >
250 >                for (int l = 0; l <= lMax_; l++) {
251 >                  sphericalHarmonic.setL(l);
252 >                  for(int m = -l; m <= l; m++){
253 >                    sphericalHarmonic.setM(m);
254 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
255 >                  }
256 >                }
257 >                nBonds++;
258 >              }  
259 >            }
260            }
261          }
262          
263 <        // Normalize Qbar
264 <        for (int m = -lNumber_;m <= lNumber_; m++){
265 <          QBar_lm[m] /= nBonds;
263 >        
264 >        for (int l = 0; l <= lMax_; l++) {        
265 >          q_l[l] = 0.0;
266 >          for(int m = -l; m <= l; m++) {
267 >            q_l[l] += norm(q[std::make_pair(l,m)]);
268 >          }    
269 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
270 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
271          }
272  
273          // Find second order invariant Q_l
274 <
275 <        QSq_l = 0.0;
276 <        for (int m = -lNumber_; m <= lNumber_; m++){
277 <          QSq_l += pow(QBar_lm[m], 2);  
274 >        
275 >        for (int l = 0; l <= lMax_; l++) {
276 >          q2[l] = 0.0;
277 >          for (int m = -l; m <= l; m++){
278 >            q2[l] += norm(q[std::make_pair(l,m)]);
279 >          }
280 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
281 >                        (RealType)(2*l + 1))/(RealType)nBonds;
282          }
193 –        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
194 –    
195 –        // 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 m2Min, m2Max;
289 <        int error, m1, m2, m3;
290 <        
291 <        W_l_ = 0.0;
292 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
293 <          // Zero work array
294 <          for (int ii = 0; ii < mSize_; ii+){
295 <            THRCOF[i] = 0.0;
284 >        // Find Third Order Invariant W_l
285 >    
286 >        for (int l = 0; l <= lMax_; l++) {
287 >          w[l] = 0.0;
288 >          for (int m1 = -l; m1 <= l; m1++) {
289 >            std::pair<int,int> lm = std::make_pair(l, m1);
290 >            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
291 >              int m2 = m2Min[lm] + mmm;
292 >              int m3 = -m1-m2;
293 >              w[l] += w3j[lm][mmm] * q[lm] *
294 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
295 >            }
296            }
297 <          // Get Wigner coefficients
298 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
212 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
213 <            m2 = floor(m2Min) + m_index - 1;
214 <            m3 = -m1-m2;
215 <            W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
216 <          }
297 >          
298 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
299          }
300  
301 <        W_l_hat = W_l_ / pow(QSq_l, 1.5);
302 <
303 <        // accumulate histogram data for Q_l and W_l_hat:
304 <
305 <        collectHistogram(Q_l, W_l_hat);
306 <                
301 >        collectHistogram(q_l, w_hat);
302 >        
303 >        Nbonds += nBonds;
304 >        for (int l = 0; l <= lMax_;  l++) {
305 >          for (int m = -l; m <= l; m++) {
306 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
307 >          }
308 >        }
309        }
310      }
311 +      
312 +    // Normalize Qbar2
313 +    for (int l = 0; l <= lMax_; l++) {
314 +      for (int m = -l; m <= l; m++){
315 +        QBar[std::make_pair(l,m)] /= Nbonds;
316 +      }
317 +    }
318      
319 <    // Normalize by number of frames
320 <    for (int m = -lNumber_; m <= lNumber_; m++){
321 <      QBar_lm[m] /=  nFrames;  
319 >    // Find second order invariant Q_l
320 >    
321 >    for (int l = 0; l <= lMax_; l++) {
322 >      Q2[l] = 0.0;
323 >      for (int m = -l; m <= l; m++){
324 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
325 >      }
326 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
327      }
328      
329 <    
234 <    
235 <    
236 <    
237 <    writeOrderParameter();
329 >    // Find Third Order Invariant W_l
330      
331 +    for (int l = 0; l <= lMax_; l++) {
332 +      W[l] = 0.0;
333 +      for (int m1 = -l; m1 <= l; m1++) {
334 +        std::pair<int,int> lm = std::make_pair(l, m1);
335 +        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
336 +          int m2 = m2Min[lm] + mmm;
337 +          int m3 = -m1-m2;
338 +          W[l] += w3j[lm][mmm] * QBar[lm] *
339 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
340 +        }
341 +      }
342 +      
343 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
344 +    }
345 +    
346 +    writeOrderParameter(Q, W_hat);    
347    }
348  
349 <  
350 <  void BondOrderParameter::processHistogram() {
243 <    
244 <    int nPairs = getNPairs();
245 <    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
246 <    RealType pairDensity = nPairs /volume * 2.0;
247 <    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
349 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
350 >                                            std::vector<ComplexType> what) {
351  
352 <    for(int i = 0 ; i < histogram_.size(); ++i){
352 >    for (int l = 0; l <= lMax_; l++) {
353 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
354 >        int qbin = (q[l] - MinQ_) / deltaQ_;
355 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
356 >        Qcount_[l]++;      
357 >      } else {
358 >        sprintf( painCave.errMsg,
359 >                 "q_l value outside reasonable range\n");
360 >        painCave.severity = OOPSE_ERROR;
361 >        painCave.isFatal = 1;
362 >        simError();  
363 >      }
364 >    }
365  
366 <      RealType rLower = i * deltaR_;
367 <      RealType rUpper = rLower + deltaR_;
368 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
369 <      RealType nIdeal = volSlice * pairConstant;
370 <
371 <      avgGofr_[i] += histogram_[i] / nIdeal;    
366 >    for (int l = 0; l <= lMax_; l++) {
367 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
368 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
369 >        W_histogram_[std::make_pair(wbin,l)] += 1;
370 >        Wcount_[l]++;      
371 >      } else {
372 >        sprintf( painCave.errMsg,
373 >                 "Re[w_hat] value outside reasonable range\n");
374 >        painCave.severity = OOPSE_ERROR;
375 >        painCave.isFatal = 1;
376 >        simError();  
377 >      }
378      }
379  
380 <  }
380 >  }  
381  
261 –  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
382  
383 <    if (Q_l < Max_Q) {
384 <      int whichBin = Q_l / deltaQ_;
385 <      Q_histogram_[whichBin] += 1;
386 <    }
267 <    if (W_l_hat < Max_W) {
268 <      int whichBin = W_l_hat / deltaW_;
269 <      W_histogram_[whichBin] += 1;
270 <    }
271 <  }
272 <  
383 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
384 >                                               std::vector<ComplexType> What) {
385 >    
386 >    std::ofstream osq((getOutputFileName() + "q").c_str());
387  
388 <  void BondOrderParameter::writeOrderParameter() {
388 >    if (osq.is_open()) {
389 >      
390 >      osq << "# Bond Order Parameters\n";
391 >      osq << "# selection: (" << selectionScript_ << ")\n";
392 >      osq << "# \n";
393 >      for (int l = 0; l <= lMax_; l++) {
394 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
395 >      }
396 >      // Normalize by number of frames and write it out:
397 >      for (int i = 0; i < nBins_; ++i) {
398 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
399 >        osq << Qval;
400 >        for (int l = 0; l <= lMax_; l++) {
401 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
402 >            (RealType)Qcount_[l];
403 >        }
404 >        osq << "\n";
405 >      }
406  
407 <    std::ofstream os(getOutputFileName().c_str());
277 <    os << "#Bond Order Parameter\n";
278 <    os << "#selection: (" << selectionScript_ << ")\n";
407 >      osq.close();
408  
409 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
410 <      os <<  orderParams_[i].p2 << "\t"
411 <         <<  orderParams_[i].director[0] << "\t"
412 <         <<  orderParams_[i].director[1] << "\t"
413 <         <<  orderParams_[i].director[2] << "\t"
285 <         <<  orderParams_[i].angle << "\n";
286 <
409 >    } else {
410 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
411 >              (getOutputFileName() + "q").c_str());
412 >      painCave.isFatal = 1;
413 >      simError();  
414      }
288 –  }
415  
416 +    std::ofstream osw((getOutputFileName() + "w").c_str());
417  
418 +    if (osw.is_open()) {
419 +      osw << "# Bond Order Parameters\n";
420 +      osw << "# selection: (" << selectionScript_ << ")\n";
421 +      osw << "# \n";
422 +      for (int l = 0; l <= lMax_; l++) {
423 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
424 +      }
425 +      // Normalize by number of frames and write it out:
426 +      for (int i = 0; i < nBins_; ++i) {
427 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
428 +        osw << Wval;
429 +        for (int l = 0; l <= lMax_; l++) {
430 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
431 +            (RealType)Wcount_[l];
432 +        }
433 +        osw << "\n";
434 +      }
435  
436 +      osw.close();
437 +    } else {
438 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
439 +              (getOutputFileName() + "w").c_str());
440 +      painCave.isFatal = 1;
441 +      simError();  
442 +    }
443 +      
444 +  }
445   }

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