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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 3017 by gezelter, Fri Sep 22 01:36:27 2006 UTC vs.
Revision 3022 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_ = 3.0;
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> q_lm;
119 <    std::map<int,ComplexType> QBar_lm;
120 <    RealType QSq_l;
121 <    RealType Q_l;
122 <    ComplexType W_l;
123 <    ComplexType W_l_hat;
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  
133 –    // Set the l for the spherical harmonic, it doesn't change
134 –    sphericalHarmonic.setL(lNumber_);
135 –
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 163 | Line 175 | namespace oopse {
175  
176          myIndex = sd->getGlobalIndex();
177          nBonds = 0;
178 <        for (int m = -lNumber_; m <= lNumber_; m++) {
179 <          q_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 191 | 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 <                  q_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                }  
219              }
220            }
221          }
222 <        RealType ql = 0.0;
223 <        for(int m=-lNumber_; m<=lNumber_; m++) {          
224 <          ql += norm(QBar_lm[m]);
225 <        }        
226 <        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
227 <        collectHistogram(sqrt(ql)/(RealType)nBonds);
222 >        
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 +        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 +        }
243 +
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 +          
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 m=-lNumber_; m<=lNumber_; m++) {
278 <          QBar_lm[m] += q_lm[m];
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 <
284 >      
285      // Normalize Qbar2
286 <    for (int m = -lNumber_;m <= lNumber_; m++){
287 <      QBar_lm[m] /= Nbonds;
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 <    QSq_l = 0.0;
295 <    for (int m = -lNumber_; m <= lNumber_; m++){
296 <      QSq_l += norm(QBar_lm[m]);
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      }
229 –    
230 –    std::cout << "qsl = " << QSq_l << "\n";
231 –    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
301      
302      // Find Third Order Invariant W_l
303      
304 <    W_l = 0.0;
305 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
306 <      // Zero work array
307 <      for (int ii = 0; ii < mSize_; ii++){
308 <        THRCOF[ii] = 0.0;
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        }
241 –      // Get Wigner coefficients
242 –      m1Pass = (double)m1;
328        
329 <      Wigner3jm(&l_, &l_, &l_,
245 <                &m1Pass, &m2Min, &m2Max,
246 <                THRCOF, &mSize_, &error);
247 <      
248 <      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
249 <        m2 = (int)floor(m2Min) + mmm;
250 <        m3 = -m1-m2;
251 <        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
252 <      }
329 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
330      }
331      
332 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
256 <    
257 <    writeOrderParameter(Q_l, real(W_l_hat));    
332 >    writeOrderParameter(Q, W_hat);    
333    }
334  
335 <  void BondOrderParameter::collectHistogram(RealType q_l) {
335 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336 >                                            std::vector<ComplexType> what) {
337  
338 <    if (q_l >= MinQ_ && q_l < MaxQ_) {
339 <      int qbin = (q_l - MinQ_) / deltaQ_;
340 <      Q_histogram_[qbin] += 1;
341 <      Qcount_++;
342 <      sumQ_ += q_l;
343 <      sumQ2_ += q_l * q_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();  
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 +    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  
368  
369 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
369 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370 >                                               std::vector<ComplexType> What) {
371 >    
372 >    std::ofstream osq((getOutputFileName() + "q").c_str());
373  
374 <    std::ofstream os(getOutputFileName().c_str());
282 <
283 <    if (os.is_open()) {
374 >    if (osq.is_open()) {
375        
376 <      os << "# Bond Order Parameters\n";
377 <      os << "# selection: (" << selectionScript_ << ")\n";
378 <      os << "# \n";
379 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
380 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
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 < Q_histogram_.size(); ++i) {
384 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
385 <        osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\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  
392 <      os.close();
392 >      osq.close();
393  
394      } else {
395        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396 <              getOutputFileName().c_str());
396 >              (getOutputFileName() + "q").c_str());
397        painCave.isFatal = 1;
398        simError();  
399      }
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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