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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 3010 by gezelter, Wed Sep 20 22:16:23 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/SphericalHarmonic.hpp"
54  
55   namespace oopse {
56  
57    BondOrderParameter::BondOrderParameter(SimInfo* info,
58                                           const std::string& filename,
59                                           const std::string& sele,
60 <                                         double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
60 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61      
62      setOutputName(getPrefix(filename) + ".bo");
63  
# Line 69 | Line 68 | namespace oopse {
68  
69      // Set up cutoff radius and order of the Legendre Polynomial:
70  
72 –    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      // Q can take values from 0 to 1
77  
78      MinQ_ = 0.0;
79 <    MaxQ_ = 1.0;
79 >    MaxQ_ = 1.1;
80      deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81 –    Q_histogram_.resize(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_ = -0.18;
86 <    MaxW_ = 0.18;
85 >    MinW_ = -0.25;
86 >    MaxW_ = 0.25;
87      deltaW_ = (MaxW_ - MinW_) / nbins;
89 –    W_histogram_.resize(nbins);
88  
89 <  }
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 +    Vector3d vec;
147      RealType costheta;
148      RealType phi;
149      RealType r;
150      RealType dist;
151 <    std::map<int, ComplexType> QBar_lm;
152 <    RealType QSq_l;
153 <    RealType Q_l;
154 <    int nBonds;
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;
121 –  
122 –    // Set the l for the spherical harmonic, it doesn't change
123 –    sphericalHarmonic.setL(lNumber_);
164  
125 –
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_++;
# Line 144 | 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
155 <
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 166 | 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);
172 <            
173 <            // Calculate "bonds" and build Q_lm(r) where
174 <            //      Q_lm = Y_lm(theta(r),phi(r))                
175 <            // The spherical harmonics are wrt any arbitrary coordinate
176 <            // system, we choose standard spherical coordinates
177 <            
178 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
179 <            
180 <            // Check to see if neighbor is in bond cutoff
181 <            
182 <            if (r < rCut_) {            
183 <              costheta = vec.z() / r;
184 <              phi = atan2(vec.y(), vec.x());
221 >              vec = sd->getPos() - atom->getPos();      
222 >              currentSnapshot_->wrapVector(vec);
223                
224 <              for(int m = -lNumber_; m <= lNumber_; m++){
225 <                sphericalHarmonic.setM(m);
226 <                QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
227 <              }
228 <              nBonds++;
229 <            }  
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 Qbar2
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 += norm(QBar_lm[m]);
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          }
206 –        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
207 –    
208 –        // 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 m1Pass, m2Min, m2Max;
276 <        int error, m1, m2, m3;
277 <
278 <        ComplexType W_l;
279 <        ComplexType W_l_hat;
280 <        W_l = 0.0;
281 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
282 <          // Zero work array
222 <          for (int ii = 0; ii < mSize_; ii++){
223 <            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 <          m1Pass = (double)m1;
227 <          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
228 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
229 <            m2 = floor(m2Min) + m_index - 1;
230 <            m3 = -m1-m2;
231 <            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
232 <          }
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, real(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 <    writeOrderParameter();
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 +    // 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 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 +                                            std::vector<ComplexType> what) {
338  
339 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
340 <
341 <    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
342 <      int qbin = (Q_l - MinQ_) / deltaQ_;
343 <      Q_histogram_[qbin] += 1;
344 <      Qcount_++;
345 <      sumQ_ += Q_l;
346 <      sumQ2_ += Q_l * Q_l;
347 <    } else {
348 <      sprintf( painCave.errMsg,
349 <               "Q_l value outside reasonable range\n");
350 <      painCave.severity = OOPSE_ERROR;
261 <      painCave.isFatal = 1;
262 <      simError();  
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 <    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
354 <      int wbin = (W_l_hat - MinW_) / deltaW_;
355 <      W_histogram_[wbin] += 1;
356 <      Wcount_++;
357 <      sumW_  += W_l_hat;
358 <      sumW2_ += W_l_hat*W_l_hat;
359 <    } else {
360 <      sprintf( painCave.errMsg,
361 <               "W_l_hat value outside reasonable range\n");
362 <      painCave.severity = OOPSE_ERROR;
363 <      painCave.isFatal = 1;
364 <      simError();  
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    }  
368  
280 –  void BondOrderParameter::writeOrderParameter() {
369  
370 +  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 +                                               std::vector<ComplexType> What) {
372 +    
373      std::ofstream osq((getOutputFileName() + "q").c_str());
374  
375      if (osq.is_open()) {
285 –
286 –      RealType qAvg = sumQ_ / (RealType) Qcount_;
287 –      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
376        
377 <      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
377 >      osq << "# Bond Order Parameters\n";
378        osq << "# selection: (" << selectionScript_ << ")\n";
379 <      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
380 <      osq << "# std. dev.: " << qStdDev << "\n";
381 <      
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 < Q_histogram_.size(); ++i) {
385 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386 <        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
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 <      
392 >
393        osq.close();
394 +
395      } else {
396        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
397                (getOutputFileName() + "q").c_str());
# Line 308 | Line 402 | namespace oopse {
402      std::ofstream osw((getOutputFileName() + "w").c_str());
403  
404      if (osw.is_open()) {
405 <
312 <      RealType wAvg = sumW_ / (RealType) Wcount_;
313 <      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
314 <      
315 <      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
405 >      osw << "# Bond Order Parameters\n";
406        osw << "# selection: (" << selectionScript_ << ")\n";
407 <      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
408 <      osw << "# std. dev.: " << wStdDev << "\n";
409 <      
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 < W_histogram_.size(); ++i) {
413 <        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
414 <        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
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 <      
420 >
421        osw.close();
422      } else {
423        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
# Line 330 | Line 425 | namespace oopse {
425        painCave.isFatal = 1;
426        simError();  
427      }
428 +      
429    }
430   }

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