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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 3018 by gezelter, Fri Sep 22 01:41:11 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_ = 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);
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() {
# Line 114 | Line 148 | namespace oopse {
148      RealType phi;
149      RealType r;
150      RealType dist;
151 <    std::map<int,ComplexType> q_lm;
152 <    std::map<int,ComplexType> QBar_lm;
153 <    RealType QSq_l;
154 <    RealType Q_l;
155 <    ComplexType W_l;
156 <    ComplexType W_l_hat;
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;
126 –    // Make arrays for Wigner3jm
127 –    double* THRCOF = new double[mSize_];
128 –    // Variables for Wigner routine
129 –    double l_ = (double)lNumber_;
130 –    double m1Pass, m2Min, m2Max;
131 –    int error, m1, m2, m3;
164  
133 –    // Set the l for the spherical harmonic, it doesn't change
134 –    sphericalHarmonic.setL(lNumber_);
135 –
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 163 | Line 202 | namespace oopse {
202  
203          myIndex = sd->getGlobalIndex();
204          nBonds = 0;
205 <        for (int m = -lNumber_; m <= lNumber_; m++) {
206 <          q_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 191 | Line 233 | namespace oopse {
233                if (r < rCut_) {
234                  costheta = vec.z() / r;
235                  phi = atan2(vec.y(), vec.x());
236 <                
237 <                for(int m = -lNumber_; m <= lNumber_; m++){
238 <                  sphericalHarmonic.setM(m);
239 <                  q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
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 <        RealType ql = 0.0;
250 <        for(int m=-lNumber_; m<=lNumber_; m++) {          
251 <          ql += norm(QBar_lm[m]);
252 <        }        
253 <        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
254 <        collectHistogram(sqrt(ql)/(RealType)nBonds);
249 >        
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 +        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 +        }
270 +
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 +          
285 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
286 +        }
287 +
288 +        collectHistogram(q_l, w_hat);
289 +        
290          Nbonds += nBonds;
291 <        for (int m=-lNumber_; m<=lNumber_; m++) {
292 <          QBar_lm[m] += q_lm[m];
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 <
298 >      
299      // Normalize Qbar2
300 <    for (int m = -lNumber_;m <= lNumber_; m++){
301 <      QBar_lm[m] /= Nbonds;
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      // Find second order invariant Q_l
307      
308 <    QSq_l = 0.0;
309 <    for (int m = -lNumber_; m <= lNumber_; m++){
310 <      QSq_l += norm(QBar_lm[m]);
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      
230 –    std::cout << "qsl = " << QSq_l << "\n";
231 –    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
232 –    
316      // Find Third Order Invariant W_l
317      
318 <    W_l = 0.0;
319 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
320 <      // Zero work array
321 <      for (int ii = 0; ii < mSize_; ii++){
322 <        THRCOF[ii] = 0.0;
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        }
241 –      // Get Wigner coefficients
242 –      m1Pass = (double)m1;
329        
330 <      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 <      }
330 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
331      }
332      
333 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
256 <    
257 <    writeOrderParameter(Q_l, real(W_l_hat));    
333 >    writeOrderParameter(Q, W_hat);    
334    }
335  
336 <  void BondOrderParameter::collectHistogram(RealType q_l) {
336 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 >                                            std::vector<ComplexType> what) {
338  
339 <    if (q_l >= MinQ_ && q_l < MaxQ_) {
340 <      int qbin = (q_l - MinQ_) / deltaQ_;
341 <      Q_histogram_[qbin] += 1;
342 <      Qcount_++;
343 <      sumQ_ += q_l;
344 <      sumQ2_ += q_l * q_l;
345 <    } else {
346 <      sprintf( painCave.errMsg,
347 <               "q_l value outside reasonable range\n");
348 <      painCave.severity = OOPSE_ERROR;
349 <      painCave.isFatal = 1;
350 <      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 +    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  
369  
370 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
370 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 >                                               std::vector<ComplexType> What) {
372 >    
373 >    std::ofstream osq((getOutputFileName() + "q").c_str());
374  
375 <    std::ofstream os(getOutputFileName().c_str());
282 <
283 <    if (os.is_open()) {
375 >    if (osq.is_open()) {
376        
377 <      os << "# Bond Order Parameters\n";
378 <      os << "# selection: (" << selectionScript_ << ")\n";
379 <      os << "# \n";
380 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
381 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
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 < Q_histogram_.size(); ++i) {
385 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386 <        os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\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  
393 <      os.close();
393 >      osq.close();
394  
395      } else {
396        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
397 <              getOutputFileName().c_str());
397 >              (getOutputFileName() + "q").c_str());
398        painCave.isFatal = 1;
399        simError();  
400      }
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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