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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 3008 by gezelter, Tue Sep 19 21:20:15 2006 UTC vs.
Revision 3024 by gezelter, Tue Sep 26 14:33:56 2006 UTC

# Line 51 | Line 51
51   #include "io/DumpReader.hpp"
52   #include "primitives/Molecule.hpp"
53   #include "utils/NumericConstant.hpp"
54 < #include "math/RealSphericalHarmonic.hpp"
54 >
55   namespace oopse {
56  
57 –
57    BondOrderParameter::BondOrderParameter(SimInfo* info,
58                                           const std::string& filename,
59                                           const std::string& sele,
60 <                                         double rCut, int lNumber, int nbins)
62 <    : StaticAnalyser(info, filename), selectionScript_(sele),
63 <      evaluator_(info), seleMan_(info){
60 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61      
62 <    setOutputName(getPrefix(filename) + ".obo");
62 >    setOutputName(getPrefix(filename) + ".bo");
63  
64      evaluator_.loadScriptString(sele);
65      if (!evaluator_.isDynamic()) {
# Line 71 | Line 68 | namespace oopse {
68  
69      // Set up cutoff radius and order of the Legendre Polynomial:
70  
74 –    lNumber_ = lNumber;
71      rCut_ = rCut;
72 <    mSize_ = 2*lNumber_+1;    
72 >    nBins_ = nbins;
73 >    Qcount_.resize(lMax_+1);
74 >    Wcount_.resize(lMax_+1);
75  
76 <    deltaQ_ = 1.0 / nbins;
79 <    deltaW_ = 2.0 / nbins;
76 >    // Q can take values from 0 to 1
77  
78 <    Q_histogram_.resize(nbins);
79 <    W_histogram_.resize(nbins);
78 >    MinQ_ = 0.0;
79 >    MaxQ_ = 1.1;
80 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81  
82 +    // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
83 +    // use values for MinW_ and MaxW_ that are slightly larger than this:
84 +
85 +    MinW_ = -0.25;
86 +    MaxW_ = 0.25;
87 +    deltaW_ = (MaxW_ - MinW_) / nbins;
88 +
89 +    // Make arrays for Wigner3jm
90 +    double* THRCOF = new double[2*lMax_+1];
91 +    // Variables for Wigner routine
92 +    double lPass, m1Pass, m2m, m2M;
93 +    int error, mSize;
94 +    mSize = 2*lMax_+1;
95 +
96 +    for (int l = 0; l <= lMax_; l++) {
97 +      lPass = (double)l;
98 +      for (int m1 = -l; m1 <= l; m1++) {
99 +        m1Pass = (double)m1;
100 +
101 +        std::pair<int,int> lm = std::make_pair(l, m1);
102 +        
103 +        // Zero work array
104 +        for (int ii = 0; ii < 2*l + 1; ii++){
105 +          THRCOF[ii] = 0.0;
106 +        }
107 +            
108 +        // Get Wigner coefficients
109 +        Wigner3jm(&lPass, &lPass, &lPass,
110 +                  &m1Pass, &m2m, &m2M,
111 +                  THRCOF, &mSize, &error);
112 +        
113 +        m2Min[lm] = (int)floor(m2m);
114 +        m2Max[lm] = (int)floor(m2M);
115 +        
116 +        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
117 +          w3j[lm].push_back(THRCOF[mmm]);
118 +        }
119 +      }
120 +    }
121    }
122 +  
123 +  BondOrderParameter::~BondOrderParameter() {
124 +    Q_histogram_.clear();
125 +    W_histogram_.clear();
126 +  }
127  
128    void BondOrderParameter::initalizeHistogram() {
129 <    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
130 <    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
129 >    for (int bin = 0; bin < nBins_; bin++) {
130 >      for (int l = 0; l <= lMax_; l++) {
131 >        Q_histogram_[std::make_pair(bin,l)] = 0;
132 >        W_histogram_[std::make_pair(bin,l)] = 0;
133 >      }
134 >    }
135    }
136  
137    void BondOrderParameter::process() {
138      Molecule* mol;
139      Atom* atom;
140      RigidBody* rb;
141 +    int myIndex;
142      SimInfo::MoleculeIterator mi;
143      Molecule::RigidBodyIterator rbIter;
144      Molecule::AtomIterator ai;
145      StuntDouble* sd;
146 <    RealType theta;
146 >    Vector3d vec;
147 >    RealType costheta;
148      RealType phi;
149      RealType r;
150      RealType dist;
151 <    std::map<int, RealType> QBar_lm;
152 <    RealType QSq_l;
153 <    RealType Q_l;
154 <    int nBonds;
155 <    RealSphericalHarmonic sphericalHarmonic;
151 >    std::map<std::pair<int,int>,ComplexType> q;
152 >    std::vector<RealType> q_l;
153 >    std::vector<RealType> q2;
154 >    std::vector<ComplexType> w;
155 >    std::vector<ComplexType> w_hat;
156 >    std::map<std::pair<int,int>,ComplexType> QBar;
157 >    std::vector<RealType> Q2;
158 >    std::vector<RealType> Q;
159 >    std::vector<ComplexType> W;
160 >    std::vector<ComplexType> W_hat;
161 >    int nBonds, Nbonds;
162 >    SphericalHarmonic sphericalHarmonic;
163      int i, j;
109 –  
110 –    // Set the l for the spherical harmonic, it doesn't change
111 –    sphericalHarmonic.setL(lNumber_);
164  
113 –
165      DumpReader reader(info_, dumpFilename_);    
166      int nFrames = reader.getNFrames();
167 +    frameCounter_ = 0;
168  
169 +    q_l.resize(lMax_+1);
170 +    q2.resize(lMax_+1);
171 +    w.resize(lMax_+1);
172 +    w_hat.resize(lMax_+1);
173  
174 +    Q2.resize(lMax_+1);
175 +    Q.resize(lMax_+1);
176 +    W.resize(lMax_+1);
177 +    W_hat.resize(lMax_+1);
178 +
179      for (int istep = 0; istep < nFrames; istep += step_) {
180        reader.readFrame(istep);
181 +      frameCounter_++;
182        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
183        
184        if (evaluator_.isDynamic()) {
# Line 131 | Line 193 | namespace oopse {
193               rb = mol->nextRigidBody(rbIter)) {
194            rb->updateAtoms();
195          }        
196 <      }      
197 <      
196 >      }          
197 >            
198        // outer loop is over the selected StuntDoubles:
199  
200        for (sd = seleMan_.beginSelected(i); sd != NULL;
201             sd = seleMan_.nextSelected(i)) {
202  
203 <        // For this central atom, zero out nBonds and QBar_lm
142 <
203 >        myIndex = sd->getGlobalIndex();
204          nBonds = 0;
205 <      
206 <        for (int m = -lNumber_; m <= lNumber_; m++) {
207 <          QBar_lm[m] = 0.0;
205 >        
206 >        for (int l = 0; l <= lMax_; l++) {
207 >          for (int m = -l; m <= l; m++) {
208 >            q[std::make_pair(l,m)] = 0.0;
209 >          }
210          }
211          
212          // inner loop is over all other atoms in the system:
# Line 153 | Line 216 | namespace oopse {
216            for (atom = mol->beginAtom(ai); atom != NULL;
217                 atom = mol->nextAtom(ai)) {
218  
219 +            if (atom->getGlobalIndex() != myIndex) {
220  
221 <            Vector3d vec = sd->getPos() - atom->getPos();      
222 <            currentSnapshot_->wrapVector(vec);
223 <            
224 <            // Calculate "bonds" and build Q_lm(r) where
225 <            //      Q_lm = Y_lm(theta(r),phi(r))                
226 <            // The spherical harmonics are wrt any arbitrary coordinate
227 <            // system, we choose standard spherical coordinates
228 <            
229 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
230 <            
231 <            // Check to see if neighbor is in bond cutoff
232 <            
233 <            if (r < rCut_) {            
234 <              theta = atan2(vec.y(), vec.x());
235 <              phi = acos(vec.z()/r);
236 <              for(int m = -lNumber_; m <= lNumber_; m++){
237 <                sphericalHarmonic.setM(m);
238 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
239 <              }
240 <              nBonds++;
241 <            }  
221 >              vec = sd->getPos() - atom->getPos();      
222 >              currentSnapshot_->wrapVector(vec);
223 >              
224 >              // Calculate "bonds" and build Q_lm(r) where
225 >              //      Q_lm = Y_lm(theta(r),phi(r))                
226 >              // The spherical harmonics are wrt any arbitrary coordinate
227 >              // system, we choose standard spherical coordinates
228 >              
229 >              r = vec.length();
230 >              
231 >              // Check to see if neighbor is in bond cutoff
232 >              
233 >              if (r < rCut_) {
234 >                costheta = vec.z() / r;
235 >                phi = atan2(vec.y(), vec.x());
236 >
237 >                for (int l = 0; l <= lMax_; l++) {
238 >                  sphericalHarmonic.setL(l);
239 >                  for(int m = -l; m <= l; m++){
240 >                    sphericalHarmonic.setM(m);
241 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
242 >                  }
243 >                }
244 >                nBonds++;
245 >              }  
246 >            }
247            }
248          }
249          
250 <        // Normalize Qbar
251 <        for (int m = -lNumber_;m <= lNumber_; m++){
252 <          QBar_lm[m] /= nBonds;
250 >        
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 <
262 <        QSq_l = 0.0;
263 <        for (int m = -lNumber_; m <= lNumber_; m++){
264 <          QSq_l += pow(QBar_lm[m], 2);  
261 >        
262 >        for (int l = 0; l <= lMax_; l++) {
263 >          q2[l] = 0.0;
264 >          for (int m = -l; m <= l; m++){
265 >            q2[l] += norm(q[std::make_pair(l,m)]);
266 >          }
267 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
268 >                        (RealType)(2*l + 1))/(RealType)nBonds;
269          }
192 –        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
193 –    
194 –        // Find Third Order Invariant W_l
270  
271 <        // Make arrays for Wigner3jm
272 <        double* THRCOF = new double[mSize_];
273 <        // Variables for Wigner routine
274 <        double l_ = (double)lNumber_;
275 <        double m2Min, m2Max;
276 <        int error, m1, m2, m3;
277 <
278 <        RealType W_l;
279 <        RealType W_l_hat;
280 <        W_l = 0.0;
281 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
282 <          // Zero work array
208 <          for (int ii = 0; ii < mSize_; ii++){
209 <            THRCOF[i] = 0.0;
271 >        // Find Third Order Invariant W_l
272 >    
273 >        for (int l = 0; l <= lMax_; l++) {
274 >          w[l] = 0.0;
275 >          for (int m1 = -l; m1 <= l; m1++) {
276 >            std::pair<int,int> lm = std::make_pair(l, m1);
277 >            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
278 >              int m2 = m2Min[lm] + mmm;
279 >              int m3 = -m1-m2;
280 >              w[l] += w3j[lm][mmm] * q[lm] *
281 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
282 >            }
283            }
284 <          // Get Wigner coefficients
285 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
213 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
214 <            m2 = floor(m2Min) + m_index - 1;
215 <            m3 = -m1-m2;
216 <            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
217 <          }
284 >          
285 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
286          }
287  
288 <        W_l_hat = W_l / pow(QSq_l, 1.5);
289 <
290 <        // accumulate histogram data for Q_l and W_l_hat:
291 <
292 <        collectHistogram(Q_l, W_l_hat);
293 <                
288 >        collectHistogram(q_l, w_hat);
289 >        
290 >        Nbonds += nBonds;
291 >        for (int l = 0; l <= lMax_;  l++) {
292 >          for (int m = -l; m <= l; m++) {
293 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
294 >          }
295 >        }
296        }
297      }
298 +      
299 +    // Normalize Qbar2
300 +    for (int l = 0; l <= lMax_; l++) {
301 +      for (int m = -l; m <= l; m++){
302 +        QBar[std::make_pair(l,m)] /= Nbonds;
303 +      }
304 +    }
305      
306 <    // Normalize by number of frames
307 <    for (int m = -lNumber_; m <= lNumber_; m++){
308 <      QBar_lm[m] /=  nFrames;  
306 >    // Find second order invariant Q_l
307 >    
308 >    for (int l = 0; l <= lMax_; l++) {
309 >      Q2[l] = 0.0;
310 >      for (int m = -l; m <= l; m++){
311 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
312 >      }
313 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
314      }
315      
316 <    
235 <    
236 <    
237 <    
238 <    writeOrderParameter();
316 >    // Find Third Order Invariant W_l
317      
318 +    for (int l = 0; l <= lMax_; l++) {
319 +      W[l] = 0.0;
320 +      for (int m1 = -l; m1 <= l; m1++) {
321 +        std::pair<int,int> lm = std::make_pair(l, m1);
322 +        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
323 +          int m2 = m2Min[lm] + mmm;
324 +          int m3 = -m1-m2;
325 +          W[l] += w3j[lm][mmm] * QBar[lm] *
326 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
327 +        }
328 +      }
329 +      
330 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
331 +    }
332 +    
333 +    writeOrderParameter(Q, W_hat);    
334    }
335  
336 <  
337 <  void BondOrderParameter::processHistogram() {
244 <    
245 <    int nPairs = getNPairs();
246 <    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
247 <    RealType pairDensity = nPairs /volume * 2.0;
248 <    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
336 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 >                                            std::vector<ComplexType> what) {
338  
339 <    for(int i = 0 ; i < histogram_.size(); ++i){
339 >    for (int l = 0; l <= lMax_; l++) {
340 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
341 >        int qbin = (q[l] - MinQ_) / deltaQ_;
342 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
343 >        Qcount_[l]++;      
344 >      } else {
345 >        sprintf( painCave.errMsg,
346 >                 "q_l value outside reasonable range\n");
347 >        painCave.severity = OOPSE_ERROR;
348 >        painCave.isFatal = 1;
349 >        simError();  
350 >      }
351 >    }
352  
353 <      RealType rLower = i * deltaR_;
354 <      RealType rUpper = rLower + deltaR_;
355 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
356 <      RealType nIdeal = volSlice * pairConstant;
357 <
358 <      avgGofr_[i] += histogram_[i] / nIdeal;    
353 >    for (int l = 0; l <= lMax_; l++) {
354 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
355 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
356 >        W_histogram_[std::make_pair(wbin,l)] += 1;
357 >        Wcount_[l]++;      
358 >      } else {
359 >        sprintf( painCave.errMsg,
360 >                 "Re[w_hat] value outside reasonable range\n");
361 >        painCave.severity = OOPSE_ERROR;
362 >        painCave.isFatal = 1;
363 >        simError();  
364 >      }
365      }
366  
367 <  }
367 >  }  
368  
262 –  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
369  
370 <    if (Q_l < MaxQ_) {
371 <      int whichBin = Q_l / deltaQ_;
372 <      Q_histogram_[whichBin] += 1;
373 <    }
268 <    if (W_l_hat < MaxW_) {
269 <      int whichBin = W_l_hat / deltaW_;
270 <      W_histogram_[whichBin] += 1;
271 <    }
272 <  }
273 <  
370 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 >                                               std::vector<ComplexType> What) {
372 >    
373 >    std::ofstream osq((getOutputFileName() + "q").c_str());
374  
375 <  void BondOrderParameter::writeOrderParameter() {
375 >    if (osq.is_open()) {
376 >      
377 >      osq << "# Bond Order Parameters\n";
378 >      osq << "# selection: (" << selectionScript_ << ")\n";
379 >      osq << "# \n";
380 >      for (int l = 0; l <= lMax_; l++) {
381 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
382 >      }
383 >      // Normalize by number of frames and write it out:
384 >      for (int i = 0; i < nBins_; ++i) {
385 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
386 >        osq << Qval;
387 >        for (int l = 0; l <= lMax_; l++) {
388 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
389 >        }
390 >        osq << "\n";
391 >      }
392  
393 <    std::ofstream os(getOutputFileName().c_str());
278 <    os << "#Bond Order Parameter\n";
279 <    os << "#selection: (" << selectionScript_ << ")\n";
393 >      osq.close();
394  
395 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
396 <      os <<  orderParams_[i].p2 << "\t"
397 <         <<  orderParams_[i].director[0] << "\t"
398 <         <<  orderParams_[i].director[1] << "\t"
399 <         <<  orderParams_[i].director[2] << "\t"
286 <         <<  orderParams_[i].angle << "\n";
287 <
395 >    } else {
396 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
397 >              (getOutputFileName() + "q").c_str());
398 >      painCave.isFatal = 1;
399 >      simError();  
400      }
289 –  }
401  
402 +    std::ofstream osw((getOutputFileName() + "w").c_str());
403  
404 +    if (osw.is_open()) {
405 +      osw << "# Bond Order Parameters\n";
406 +      osw << "# selection: (" << selectionScript_ << ")\n";
407 +      osw << "# \n";
408 +      for (int l = 0; l <= lMax_; l++) {
409 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
410 +      }
411 +      // Normalize by number of frames and write it out:
412 +      for (int i = 0; i < nBins_; ++i) {
413 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
414 +        osw << Wval;
415 +        for (int l = 0; l <= lMax_; l++) {
416 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
417 +        }
418 +        osw << "\n";
419 +      }
420  
421 +      osw.close();
422 +    } else {
423 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
424 +              (getOutputFileName() + "w").c_str());
425 +      painCave.isFatal = 1;
426 +      simError();  
427 +    }
428 +      
429 +  }
430   }

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