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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 1044 by gezelter, Thu Sep 21 18:04:52 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/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);
90 –
88    }
89  
90    BondOrderParameter::~BondOrderParameter() {
# Line 96 | Line 93 | namespace oopse {
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() {
# Line 114 | Line 115 | namespace oopse {
115      RealType phi;
116      RealType r;
117      RealType dist;
118 <    std::map<int, ComplexType> QBar_lm;
119 <    RealType QSq_l;
120 <    RealType Q_l;
121 <    ComplexType W_l;
122 <    ComplexType W_l_hat;
123 <    int nBonds;
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      // Make arrays for Wigner3jm
132 <    double* THRCOF = new double[mSize_];
132 >    double* THRCOF = new double[2*lMax_+1];
133      // Variables for Wigner routine
134 <    double l_ = (double)lNumber_;
135 <    double m1Pass, m2Min, m2Max;
136 <    int error, m1, m2, m3;
134 >    double lPass, m1Pass, m2Min, m2Max;
135 >    int error, m1, m2, m3, mSize;
136 >    mSize = 2*lMax_+1;
137  
132 –    // Set the l for the spherical harmonic, it doesn't change
133 –    sphericalHarmonic.setL(lNumber_);
134 –
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_++;
# Line 153 | 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          myIndex = sd->getGlobalIndex();
164 –
165 –        // For this central atom, zero out nBonds and QBar_lm
166 –
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 194 | Line 206 | namespace oopse {
206                if (r < rCut_) {
207                  costheta = vec.z() / r;
208                  phi = atan2(vec.y(), vec.x());
209 <                
210 <                for(int m = -lNumber_; m <= lNumber_; m++){
211 <                  sphericalHarmonic.setM(m);
212 <                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
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                }  
# Line 205 | Line 220 | namespace oopse {
220            }
221          }
222          
223 <        // Normalize Qbar2
224 <        for (int m = -lNumber_;m <= lNumber_; m++){
225 <          QBar_lm[m] /= nBonds;
226 <          std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
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 += norm(QBar_lm[m]);
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          }
220 –        std::cout << "qsq_l = " << QSq_l << "\n";
221 –        Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
222 –                   (2.0*(RealType)lNumber_ + 1.0));
243  
244          // Find Third Order Invariant W_l
245 <        
246 <        W_l = 0.0;
247 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
248 <          // Zero work array
249 <          for (int ii = 0; ii < mSize_; ii++){
250 <            THRCOF[i] = 0.0;
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 <          m1Pass = (double)m1;
234 <          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
235 <          for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
236 <            m2 = floor(m2Min) + m_index - 1;
237 <            m3 = -m1-m2;
238 <            W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3];
239 <          }
270 >          
271 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
272          }
241 –        
242 –        W_l_hat = W_l / pow(QSq_l, 1.5);
243 –        
244 –        // accumulate histogram data for Q_l and W_l_hat:
273  
274 <        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
275 <        collectHistogram(Q_l, real(W_l_hat));
276 <                
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 >        }
282        }
283      }
284 <    
285 <    writeOrderParameter();
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 +    // 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 +    // 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 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336 +                                            std::vector<ComplexType> what) {
337  
338 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
339 <
340 <    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
341 <      int qbin = (Q_l - MinQ_) / deltaQ_;
342 <      Q_histogram_[qbin] += 1;
343 <      Qcount_++;
344 <      sumQ_ += Q_l;
345 <      sumQ2_ += Q_l * Q_l;
346 <    } else {
347 <      sprintf( painCave.errMsg,
348 <               "Q_l value outside reasonable range\n");
349 <      painCave.severity = OOPSE_ERROR;
269 <      painCave.isFatal = 1;
270 <      simError();  
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 <    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
353 <      int wbin = (W_l_hat - MinW_) / deltaW_;
354 <      W_histogram_[wbin] += 1;
355 <      Wcount_++;
356 <      sumW_  += W_l_hat;
357 <      sumW2_ += W_l_hat*W_l_hat;
358 <    } else {
359 <      sprintf( painCave.errMsg,
360 <               "W_l_hat value outside reasonable range\n");
361 <      painCave.severity = OOPSE_ERROR;
362 <      painCave.isFatal = 1;
363 <      simError();  
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    }  
367  
288 –  void BondOrderParameter::writeOrderParameter() {
368  
369 +  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370 +                                               std::vector<ComplexType> What) {
371 +    
372      std::ofstream osq((getOutputFileName() + "q").c_str());
373  
374      if (osq.is_open()) {
293 –
294 –      RealType qAvg = sumQ_ / (RealType) Qcount_;
295 –      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
375        
376 <      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
376 >      osq << "# Bond Order Parameters\n";
377        osq << "# selection: (" << selectionScript_ << ")\n";
378 <      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
379 <      osq << "# std. dev.: " << qStdDev << "\n";
380 <      
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 < Q_histogram_.size(); ++i) {
384 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
385 <        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
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 <      
391 >
392        osq.close();
393 +
394      } else {
395        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396                (getOutputFileName() + "q").c_str());
# Line 316 | Line 401 | namespace oopse {
401      std::ofstream osw((getOutputFileName() + "w").c_str());
402  
403      if (osw.is_open()) {
404 <
320 <      RealType wAvg = sumW_ / (RealType) Wcount_;
321 <      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
322 <      
323 <      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
404 >      osw << "# Bond Order Parameters\n";
405        osw << "# selection: (" << selectionScript_ << ")\n";
406 <      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
407 <      osw << "# std. dev.: " << wStdDev << "\n";
408 <      
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 < W_histogram_.size(); ++i) {
412 <        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
413 <        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
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 <      
419 >
420        osw.close();
421      } else {
422        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
# Line 338 | Line 424 | namespace oopse {
424        painCave.isFatal = 1;
425        simError();  
426      }
427 +      
428    }
429   }

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