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root/OpenMD/trunk/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1040 by gezelter, Tue Sep 19 21:20:15 2006 UTC vs.
Revision 1052 by gezelter, Tue Sep 26 01:30:32 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  
90 +  BondOrderParameter::~BondOrderParameter() {
91 +    Q_histogram_.clear();
92 +    W_histogram_.clear();
93 +  }
94 +
95    void BondOrderParameter::initalizeHistogram() {
96 <    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
97 <    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
96 >    for (int bin = 0; bin < nBins_; bin++) {
97 >      for (int l = 0; l <= lMax_; l++) {
98 >        Q_histogram_[std::make_pair(bin,l)] = 0;
99 >        W_histogram_[std::make_pair(bin,l)] = 0;
100 >      }
101 >    }
102    }
103  
104    void BondOrderParameter::process() {
105      Molecule* mol;
106      Atom* atom;
107      RigidBody* rb;
108 +    int myIndex;
109      SimInfo::MoleculeIterator mi;
110      Molecule::RigidBodyIterator rbIter;
111      Molecule::AtomIterator ai;
112      StuntDouble* sd;
113 <    RealType theta;
113 >    Vector3d vec;
114 >    RealType costheta;
115      RealType phi;
116      RealType r;
117      RealType dist;
118 <    std::map<int, RealType> QBar_lm;
119 <    RealType QSq_l;
120 <    RealType Q_l;
121 <    int nBonds;
122 <    RealSphericalHarmonic sphericalHarmonic;
118 >    std::map<std::pair<int,int>,ComplexType> q;
119 >    std::vector<RealType> q_l;
120 >    std::vector<RealType> q2;
121 >    std::vector<ComplexType> w;
122 >    std::vector<ComplexType> w_hat;
123 >    std::map<std::pair<int,int>,ComplexType> QBar;
124 >    std::vector<RealType> Q2;
125 >    std::vector<RealType> Q;
126 >    std::vector<ComplexType> W;
127 >    std::vector<ComplexType> W_hat;
128 >    int nBonds, Nbonds;
129 >    SphericalHarmonic sphericalHarmonic;
130      int i, j;
131 <  
132 <    // Set the l for the spherical harmonic, it doesn't change
133 <    sphericalHarmonic.setL(lNumber_);
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;
137  
113 –
138      DumpReader reader(info_, dumpFilename_);    
139      int nFrames = reader.getNFrames();
140 +    frameCounter_ = 0;
141  
142 +    q_l.resize(lMax_+1);
143 +    q2.resize(lMax_+1);
144 +    w.resize(lMax_+1);
145 +    w_hat.resize(lMax_+1);
146  
147 +    Q2.resize(lMax_+1);
148 +    Q.resize(lMax_+1);
149 +    W.resize(lMax_+1);
150 +    W_hat.resize(lMax_+1);
151 +
152      for (int istep = 0; istep < nFrames; istep += step_) {
153        reader.readFrame(istep);
154 +      frameCounter_++;
155        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
156        
157        if (evaluator_.isDynamic()) {
# Line 131 | Line 166 | namespace oopse {
166               rb = mol->nextRigidBody(rbIter)) {
167            rb->updateAtoms();
168          }        
169 <      }      
170 <      
169 >      }          
170 >            
171        // outer loop is over the selected StuntDoubles:
172  
173        for (sd = seleMan_.beginSelected(i); sd != NULL;
174             sd = seleMan_.nextSelected(i)) {
175  
176 <        // For this central atom, zero out nBonds and QBar_lm
142 <
176 >        myIndex = sd->getGlobalIndex();
177          nBonds = 0;
178 <      
179 <        for (int m = -lNumber_; m <= lNumber_; m++) {
180 <          QBar_lm[m] = 0.0;
178 >        
179 >        for (int l = 0; l <= lMax_; l++) {
180 >          for (int m = -l; m <= l; m++) {
181 >            q[std::make_pair(l,m)] = 0.0;
182 >          }
183          }
184          
185          // inner loop is over all other atoms in the system:
# Line 153 | Line 189 | namespace oopse {
189            for (atom = mol->beginAtom(ai); atom != NULL;
190                 atom = mol->nextAtom(ai)) {
191  
192 +            if (atom->getGlobalIndex() != myIndex) {
193  
194 <            Vector3d vec = sd->getPos() - atom->getPos();      
195 <            currentSnapshot_->wrapVector(vec);
196 <            
197 <            // Calculate "bonds" and build Q_lm(r) where
198 <            //      Q_lm = Y_lm(theta(r),phi(r))                
199 <            // The spherical harmonics are wrt any arbitrary coordinate
200 <            // system, we choose standard spherical coordinates
201 <            
202 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
203 <            
204 <            // Check to see if neighbor is in bond cutoff
205 <            
206 <            if (r < rCut_) {            
207 <              theta = atan2(vec.y(), vec.x());
208 <              phi = acos(vec.z()/r);
209 <              for(int m = -lNumber_; m <= lNumber_; m++){
210 <                sphericalHarmonic.setM(m);
211 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
212 <              }
213 <              nBonds++;
214 <            }  
194 >              vec = sd->getPos() - atom->getPos();      
195 >              currentSnapshot_->wrapVector(vec);
196 >              
197 >              // Calculate "bonds" and build Q_lm(r) where
198 >              //      Q_lm = Y_lm(theta(r),phi(r))                
199 >              // The spherical harmonics are wrt any arbitrary coordinate
200 >              // system, we choose standard spherical coordinates
201 >              
202 >              r = vec.length();
203 >              
204 >              // Check to see if neighbor is in bond cutoff
205 >              
206 >              if (r < rCut_) {
207 >                costheta = vec.z() / r;
208 >                phi = atan2(vec.y(), vec.x());
209 >
210 >                for (int l = 0; l <= lMax_; l++) {
211 >                  sphericalHarmonic.setL(l);
212 >                  for(int m = -l; m <= l; m++){
213 >                    sphericalHarmonic.setM(m);
214 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
215 >                  }
216 >                }
217 >                nBonds++;
218 >              }  
219 >            }
220            }
221          }
222          
223 <        // Normalize Qbar
224 <        for (int m = -lNumber_;m <= lNumber_; m++){
225 <          QBar_lm[m] /= nBonds;
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
234 <
235 <        QSq_l = 0.0;
236 <        for (int m = -lNumber_; m <= lNumber_; m++){
237 <          QSq_l += pow(QBar_lm[m], 2);  
234 >        
235 >        for (int l = 0; l <= lMax_; l++) {
236 >          q2[l] = 0.0;
237 >          for (int m = -l; m <= l; m++){
238 >            q2[l] += norm(q[std::make_pair(l,m)]);
239 >          }
240 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241 >                        (RealType)(2*l + 1))/(RealType)nBonds;
242          }
192 –        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
193 –    
194 –        // Find Third Order Invariant W_l
243  
244 <        // Make arrays for Wigner3jm
245 <        double* THRCOF = new double[mSize_];
246 <        // Variables for Wigner routine
247 <        double l_ = (double)lNumber_;
248 <        double m2Min, m2Max;
249 <        int error, m1, m2, m3;
250 <
251 <        RealType W_l;
252 <        RealType W_l_hat;
253 <        W_l = 0.0;
254 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
255 <          // Zero work array
256 <          for (int ii = 0; ii < mSize_; ii++){
257 <            THRCOF[i] = 0.0;
244 >        // Find Third Order Invariant W_l
245 >    
246 >        for (int l = 0; l <= lMax_; l++) {
247 >          w[l] = 0.0;
248 >          lPass = (double)l;
249 >          for (int m1 = -l; m1 <= l; m1++) {
250 >            // Zero work array
251 >            for (int ii = 0; ii < 2*l + 1; ii++){
252 >              THRCOF[ii] = 0.0;
253 >            }
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 >            }
269            }
270 <          // Get Wigner coefficients
271 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
272 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
273 <            m2 = floor(m2Min) + m_index - 1;
274 <            m3 = -m1-m2;
275 <            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
270 >          
271 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
272 >        }
273 >
274 >        collectHistogram(q_l, w_hat);
275 >        
276 >        Nbonds += nBonds;
277 >        for (int l = 0; l <= lMax_;  l++) {
278 >          for (int m = -l; m <= l; m++) {
279 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
280            }
281          }
219 –
220 –        W_l_hat = W_l / pow(QSq_l, 1.5);
221 –
222 –        // accumulate histogram data for Q_l and W_l_hat:
223 –
224 –        collectHistogram(Q_l, W_l_hat);
225 –                
282        }
283      }
284 +      
285 +    // Normalize Qbar2
286 +    for (int l = 0; l <= lMax_; l++) {
287 +      for (int m = -l; m <= l; m++){
288 +        QBar[std::make_pair(l,m)] /= Nbonds;
289 +      }
290 +    }
291      
292 <    // Normalize by number of frames
293 <    for (int m = -lNumber_; m <= lNumber_; m++){
294 <      QBar_lm[m] /=  nFrames;  
292 >    // Find second order invariant Q_l
293 >    
294 >    for (int l = 0; l <= lMax_; l++) {
295 >      Q2[l] = 0.0;
296 >      for (int m = -l; m <= l; m++){
297 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
298 >      }
299 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
300      }
301      
302 <    
235 <    
236 <    
237 <    
238 <    writeOrderParameter();
302 >    // Find Third Order Invariant W_l
303      
304 +    for (int l = 0; l <= lMax_; l++) {
305 +      W[l] = 0.0;
306 +      lPass = (double)l;
307 +      for (int m1 = -l; m1 <= l; m1++) {
308 +        // Zero work array
309 +        for (int ii = 0; ii < 2*l + 1; ii++){
310 +          THRCOF[ii] = 0.0;
311 +        }
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 +        }
327 +      }
328 +      
329 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
330 +    }
331 +    
332 +    writeOrderParameter(Q, W_hat);    
333    }
334  
335 <  
336 <  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;
335 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336 >                                            std::vector<ComplexType> what) {
337  
338 <    for(int i = 0 ; i < histogram_.size(); ++i){
338 >    for (int l = 0; l <= lMax_; l++) {
339 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
340 >        int qbin = (q[l] - MinQ_) / deltaQ_;
341 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
342 >        Qcount_[l]++;      
343 >      } else {
344 >        sprintf( painCave.errMsg,
345 >                 "q_l value outside reasonable range\n");
346 >        painCave.severity = OOPSE_ERROR;
347 >        painCave.isFatal = 1;
348 >        simError();  
349 >      }
350 >    }
351  
352 <      RealType rLower = i * deltaR_;
353 <      RealType rUpper = rLower + deltaR_;
354 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
355 <      RealType nIdeal = volSlice * pairConstant;
356 <
357 <      avgGofr_[i] += histogram_[i] / nIdeal;    
352 >    for (int l = 0; l <= lMax_; l++) {
353 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
354 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
355 >        W_histogram_[std::make_pair(wbin,l)] += 1;
356 >        Wcount_[l]++;      
357 >      } else {
358 >        sprintf( painCave.errMsg,
359 >                 "Re[w_hat] value outside reasonable range\n");
360 >        painCave.severity = OOPSE_ERROR;
361 >        painCave.isFatal = 1;
362 >        simError();  
363 >      }
364      }
365  
366 <  }
366 >  }  
367  
262 –  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
368  
369 <    if (Q_l < MaxQ_) {
370 <      int whichBin = Q_l / deltaQ_;
371 <      Q_histogram_[whichBin] += 1;
372 <    }
268 <    if (W_l_hat < MaxW_) {
269 <      int whichBin = W_l_hat / deltaW_;
270 <      W_histogram_[whichBin] += 1;
271 <    }
272 <  }
273 <  
369 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370 >                                               std::vector<ComplexType> What) {
371 >    
372 >    std::ofstream osq((getOutputFileName() + "q").c_str());
373  
374 <  void BondOrderParameter::writeOrderParameter() {
374 >    if (osq.is_open()) {
375 >      
376 >      osq << "# Bond Order Parameters\n";
377 >      osq << "# selection: (" << selectionScript_ << ")\n";
378 >      osq << "# \n";
379 >      for (int l = 0; l <= lMax_; l++) {
380 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
381 >      }
382 >      // Normalize by number of frames and write it out:
383 >      for (int i = 0; i < nBins_; ++i) {
384 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
385 >        osq << Qval;
386 >        for (int l = 0; l <= lMax_; l++) {
387 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
388 >        }
389 >        osq << "\n";
390 >      }
391  
392 <    std::ofstream os(getOutputFileName().c_str());
278 <    os << "#Bond Order Parameter\n";
279 <    os << "#selection: (" << selectionScript_ << ")\n";
392 >      osq.close();
393  
394 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
395 <      os <<  orderParams_[i].p2 << "\t"
396 <         <<  orderParams_[i].director[0] << "\t"
397 <         <<  orderParams_[i].director[1] << "\t"
398 <         <<  orderParams_[i].director[2] << "\t"
286 <         <<  orderParams_[i].angle << "\n";
287 <
394 >    } else {
395 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396 >              (getOutputFileName() + "q").c_str());
397 >      painCave.isFatal = 1;
398 >      simError();  
399      }
289 –  }
400  
401 +    std::ofstream osw((getOutputFileName() + "w").c_str());
402  
403 +    if (osw.is_open()) {
404 +      osw << "# Bond Order Parameters\n";
405 +      osw << "# selection: (" << selectionScript_ << ")\n";
406 +      osw << "# \n";
407 +      for (int l = 0; l <= lMax_; l++) {
408 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
409 +      }
410 +      // Normalize by number of frames and write it out:
411 +      for (int i = 0; i < nBins_; ++i) {
412 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
413 +        osw << Wval;
414 +        for (int l = 0; l <= lMax_; l++) {
415 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
416 +        }
417 +        osw << "\n";
418 +      }
419  
420 +      osw.close();
421 +    } else {
422 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
423 +              (getOutputFileName() + "w").c_str());
424 +      painCave.isFatal = 1;
425 +      simError();  
426 +    }
427 +      
428 +  }
429   }

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