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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3021 by gezelter, Mon Sep 25 22:08:33 2006 UTC vs.
Revision 3087 by gezelter, Wed Dec 20 21:03:11 2006 UTC

# Line 37 | Line 37
37   * arising out of the use of or inability to use software, even if the
38   * University of Notre Dame has been advised of the possibility of
39   * such damages.
40 + *
41 + *  BondOrderParameter.cpp
42 + *  OOPSE-4
43 + *
44 + *  Created by J. Daniel Gezelter on 09/26/06.
45 + *  @author  J. Daniel Gezelter
46 + *  @version $Id: BondOrderParameter.cpp,v 1.22 2006-12-20 21:03:11 gezelter Exp $
47 + *
48   */
41 –
42 –
43 – /* Creates orientational bond order parameters as outlined by
44 – *     Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
45 – *     Phys Rev B, 28,784,1983
46 – *
47 – */
49  
50   #include "applications/staticProps/BondOrderParameter.hpp"
51   #include "utils/simError.h"
# Line 57 | Line 58 | namespace oopse {
58    BondOrderParameter::BondOrderParameter(SimInfo* info,
59                                           const std::string& filename,
60                                           const std::string& sele,
61 <                                         double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62      
63      setOutputName(getPrefix(filename) + ".bo");
64  
# Line 68 | Line 69 | namespace oopse {
69  
70      // Set up cutoff radius and order of the Legendre Polynomial:
71  
71 –    lMax_ = lMax;
72      rCut_ = rCut;
73      nBins_ = nbins;
74      Qcount_.resize(lMax_+1);
# Line 83 | Line 83 | namespace oopse {
83      // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
84      // use values for MinW_ and MaxW_ that are slightly larger than this:
85  
86 <    MinW_ = -0.18;
87 <    MaxW_ = 0.18;
86 >    MinW_ = -1.1;
87 >    MaxW_ = 1.1;
88      deltaW_ = (MaxW_ - MinW_) / nbins;
89 –  }
89  
90 +    // Make arrays for Wigner3jm
91 +    double* THRCOF = new double[2*lMax_+1];
92 +    // Variables for Wigner routine
93 +    double lPass, m1Pass, m2m, m2M;
94 +    int error, mSize;
95 +    mSize = 2*lMax_+1;
96 +
97 +    for (int l = 0; l <= lMax_; l++) {
98 +      lPass = (double)l;
99 +      for (int m1 = -l; m1 <= l; m1++) {
100 +        m1Pass = (double)m1;
101 +
102 +        std::pair<int,int> lm = std::make_pair(l, m1);
103 +        
104 +        // Zero work array
105 +        for (int ii = 0; ii < 2*l + 1; ii++){
106 +          THRCOF[ii] = 0.0;
107 +        }
108 +
109 +        // Get Wigner coefficients
110 +        Wigner3jm(&lPass, &lPass, &lPass,
111 +                  &m1Pass, &m2m, &m2M,
112 +                  THRCOF, &mSize, &error);
113 +        
114 +        m2Min[lm] = (int)floor(m2m);
115 +        m2Max[lm] = (int)floor(m2M);
116 +        
117 +        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
118 +          w3j[lm].push_back(THRCOF[mmm]);
119 +        }
120 +      }
121 +    }
122 +    delete [] THRCOF;
123 +    THRCOF = NULL;
124 +  }
125 +  
126    BondOrderParameter::~BondOrderParameter() {
127      Q_histogram_.clear();
128      W_histogram_.clear();
129 +    for (int l = 0; l <= lMax_; l++) {
130 +      for (int m = -l; m <= l; m++) {
131 +        w3j[std::make_pair(l,m)].clear();
132 +      }
133 +    }
134 +    w3j.clear();
135 +    m2Min.clear();
136 +    m2Max.clear();
137    }
138 <
138 >  
139    void BondOrderParameter::initalizeHistogram() {
140      for (int bin = 0; bin < nBins_; bin++) {
141        for (int l = 0; l <= lMax_; l++) {
# Line 118 | Line 161 | namespace oopse {
161      RealType dist;
162      std::map<std::pair<int,int>,ComplexType> q;
163      std::vector<RealType> q_l;
164 +    std::vector<RealType> q2;
165 +    std::vector<ComplexType> w;
166 +    std::vector<ComplexType> w_hat;
167      std::map<std::pair<int,int>,ComplexType> QBar;
168      std::vector<RealType> Q2;
169      std::vector<RealType> Q;
# Line 126 | Line 172 | namespace oopse {
172      int nBonds, Nbonds;
173      SphericalHarmonic sphericalHarmonic;
174      int i, j;
129 –    // Make arrays for Wigner3jm
130 –    double* THRCOF = new double[2*lMax_+1];
131 –    // Variables for Wigner routine
132 –    double lPass, m1Pass, m2Min, m2Max;
133 –    int error, m1, m2, m3, mSize;
134 –    mSize = 2*lMax_+1;
175  
176      DumpReader reader(info_, dumpFilename_);    
177      int nFrames = reader.getNFrames();
178      frameCounter_ = 0;
179  
180      q_l.resize(lMax_+1);
181 +    q2.resize(lMax_+1);
182 +    w.resize(lMax_+1);
183 +    w_hat.resize(lMax_+1);
184 +
185      Q2.resize(lMax_+1);
186      Q.resize(lMax_+1);
187      W.resize(lMax_+1);
188      W_hat.resize(lMax_+1);
189 +    Nbonds = 0;
190  
191      for (int istep = 0; istep < nFrames; istep += step_) {
192        reader.readFrame(istep);
# Line 186 | Line 231 | namespace oopse {
231              if (atom->getGlobalIndex() != myIndex) {
232  
233                vec = sd->getPos() - atom->getPos();      
234 <              currentSnapshot_->wrapVector(vec);
234 >
235 >              if (usePeriodicBoundaryConditions_)
236 >                currentSnapshot_->wrapVector(vec);
237                
238                // Calculate "bonds" and build Q_lm(r) where
239                //      Q_lm = Y_lm(theta(r),phi(r))                
# Line 215 | Line 262 | namespace oopse {
262          }
263          
264          
265 <        for (int l = 0; l <= lMax_; l++) {        
266 <          q_l[l] = 0.0;
267 <          for(int m = -l; m <= l; m++) {
268 <            q_l[l] += norm(q[std::make_pair(l,m)]);
269 <          }    
270 <          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
271 <          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
265 >        for (int l = 0; l <= lMax_; l++) {
266 >          q2[l] = 0.0;
267 >          for (int m = -l; m <= l; m++){
268 >            q[std::make_pair(l,m)] /= (RealType)nBonds;            
269 >            q2[l] += norm(q[std::make_pair(l,m)]);
270 >          }
271 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
272          }
226 –        collectHistogram(q_l);
273          
274 +        // Find Third Order Invariant W_l
275 +    
276 +        for (int l = 0; l <= lMax_; l++) {
277 +          w[l] = 0.0;
278 +          for (int m1 = -l; m1 <= l; m1++) {
279 +            std::pair<int,int> lm = std::make_pair(l, m1);
280 +            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
281 +              int m2 = m2Min[lm] + mmm;
282 +              int m3 = -m1-m2;
283 +              w[l] += w3j[lm][mmm] * q[lm] *
284 +                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
285 +            }
286 +          }
287 +          
288 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
289 +        }
290 +
291 +        collectHistogram(q_l, w_hat);
292 +        
293          Nbonds += nBonds;
294          for (int l = 0; l <= lMax_;  l++) {
295            for (int m = -l; m <= l; m++) {
296 <            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
296 >            QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
297            }
298          }
299        }
# Line 251 | Line 316 | namespace oopse {
316        Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317      }
318      
254 –
255 –    
319      // Find Third Order Invariant W_l
320      
321      for (int l = 0; l <= lMax_; l++) {
322        W[l] = 0.0;
260 –      lPass = (double)l;
323        for (int m1 = -l; m1 <= l; m1++) {
324 <        // Zero work array
325 <        for (int ii = 0; ii < 2*l + 1; ii++){
326 <          THRCOF[ii] = 0.0;
324 >        std::pair<int,int> lm = std::make_pair(l, m1);
325 >        for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
326 >          int m2 = m2Min[lm] + mmm;
327 >          int m3 = -m1-m2;
328 >          W[l] += w3j[lm][mmm] * QBar[lm] *
329 >            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
330          }
266 –        // Get Wigner coefficients
267 –        m1Pass = (double)m1;
268 –        
269 –        Wigner3jm(&lPass, &lPass, &lPass,
270 –                  &m1Pass, &m2Min, &m2Max,
271 –                  THRCOF, &mSize, &error);
272 –        
273 –        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
274 –          m2 = (int)floor(m2Min) + mmm;
275 –          m3 = -m1-m2;
276 –          W[l] += THRCOF[mmm] *
277 –            QBar[std::make_pair(l,m1)] *
278 –            QBar[std::make_pair(l,m2)] *
279 –            QBar[std::make_pair(l,m3)];
280 –        }
331        }
332        
333        W_hat[l] = W[l] / pow(Q2[l], 1.5);
# Line 286 | Line 336 | namespace oopse {
336      writeOrderParameter(Q, W_hat);    
337    }
338  
339 <  void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
339 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340 >                                            std::vector<ComplexType> what) {
341  
342      for (int l = 0; l <= lMax_; l++) {
343        if (q[l] >= MinQ_ && q[l] < MaxQ_) {
# Line 302 | Line 353 | namespace oopse {
353        }
354      }
355  
356 +    for (int l = 0; l <= lMax_; l++) {
357 +      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358 +        int wbin = (real(what[l]) - MinW_) / deltaW_;
359 +        W_histogram_[std::make_pair(wbin,l)] += 1;
360 +        Wcount_[l]++;      
361 +      } else {
362 +        sprintf( painCave.errMsg,
363 +                 "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
364 +        painCave.severity = OOPSE_ERROR;
365 +        painCave.isFatal = 1;
366 +        simError();  
367 +      }
368 +    }
369 +
370    }  
371  
372  
373 <  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
373 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374 >                                               std::vector<ComplexType> What) {
375      
376 <    std::ofstream os(getOutputFileName().c_str());
377 <    
378 <    if (os.is_open()) {
376 >    std::ofstream osq((getOutputFileName() + "q").c_str());
377 >
378 >    if (osq.is_open()) {
379        
380 <      os << "# Bond Order Parameters\n";
381 <      os << "# selection: (" << selectionScript_ << ")\n";
380 >      osq << "# Bond Order Parameters\n";
381 >      osq << "# selection: (" << selectionScript_ << ")\n";
382 >      osq << "# \n";
383        for (int l = 0; l <= lMax_; l++) {
384 <        os << "# \n";
318 <        os << "# <Q_" << l << ">: " << Q[l] << "\n";
319 <        os << "# <W_" << l << ">: " << real(What[l]) << "\n";
384 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385        }
386        // Normalize by number of frames and write it out:
387        for (int i = 0; i < nBins_; ++i) {
388          RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
389 <        os << Qval;
389 >        osq << Qval;
390          for (int l = 0; l <= lMax_; l++) {
391 <          os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
391 >
392 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393          }
394 <        os << "\n";
394 >        osq << "\n";
395        }
396  
397 <      os.close();
397 >      osq.close();
398  
399      } else {
400        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401 <              getOutputFileName().c_str());
401 >              (getOutputFileName() + "q").c_str());
402        painCave.isFatal = 1;
403        simError();  
404      }
405 +
406 +    std::ofstream osw((getOutputFileName() + "w").c_str());
407 +
408 +    if (osw.is_open()) {
409 +      osw << "# Bond Order Parameters\n";
410 +      osw << "# selection: (" << selectionScript_ << ")\n";
411 +      osw << "# \n";
412 +      for (int l = 0; l <= lMax_; l++) {
413 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
414 +      }
415 +      // Normalize by number of frames and write it out:
416 +      for (int i = 0; i < nBins_; ++i) {
417 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
418 +        osw << Wval;
419 +        for (int l = 0; l <= lMax_; l++) {
420 +
421 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422 +        }
423 +        osw << "\n";
424 +      }
425 +
426 +      osw.close();
427 +    } else {
428 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
429 +              (getOutputFileName() + "w").c_str());
430 +      painCave.isFatal = 1;
431 +      simError();  
432 +    }
433 +      
434    }
435   }

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