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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1051 by gezelter, Mon Sep 25 22:08:33 2006 UTC vs.
Revision 1078 by gezelter, Wed Oct 18 21:58:48 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 1.19 2006-10-18 21:58:47 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_ = -0.25;
87 >    MaxW_ = 0.25;
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);
# Line 186 | Line 230 | namespace oopse {
230              if (atom->getGlobalIndex() != myIndex) {
231  
232                vec = sd->getPos() - atom->getPos();      
233 <              currentSnapshot_->wrapVector(vec);
233 >
234 >              if (usePeriodicBoundaryConditions_)
235 >                currentSnapshot_->wrapVector(vec);
236                
237                // Calculate "bonds" and build Q_lm(r) where
238                //      Q_lm = Y_lm(theta(r),phi(r))                
# Line 223 | Line 269 | namespace oopse {
269            q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
270            q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
271          }
272 <        collectHistogram(q_l);
272 >
273 >        // Find second order invariant Q_l
274          
275 +        for (int l = 0; l <= lMax_; l++) {
276 +          q2[l] = 0.0;
277 +          for (int m = -l; m <= l; m++){
278 +            q2[l] += norm(q[std::make_pair(l,m)]);
279 +          }
280 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
281 +                        (RealType)(2*l + 1))/(RealType)nBonds;
282 +        }
283 +
284 +        // Find Third Order Invariant W_l
285 +    
286 +        for (int l = 0; l <= lMax_; l++) {
287 +          w[l] = 0.0;
288 +          for (int m1 = -l; m1 <= l; m1++) {
289 +            std::pair<int,int> lm = std::make_pair(l, m1);
290 +            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
291 +              int m2 = m2Min[lm] + mmm;
292 +              int m3 = -m1-m2;
293 +              w[l] += w3j[lm][mmm] * q[lm] *
294 +                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
295 +            }
296 +          }
297 +          
298 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
299 +        }
300 +
301 +        collectHistogram(q_l, w_hat);
302 +        
303          Nbonds += nBonds;
304          for (int l = 0; l <= lMax_;  l++) {
305            for (int m = -l; m <= l; m++) {
# Line 251 | Line 326 | namespace oopse {
326        Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
327      }
328      
254 –
255 –    
329      // Find Third Order Invariant W_l
330      
331      for (int l = 0; l <= lMax_; l++) {
332        W[l] = 0.0;
260 –      lPass = (double)l;
333        for (int m1 = -l; m1 <= l; m1++) {
334 <        // Zero work array
335 <        for (int ii = 0; ii < 2*l + 1; ii++){
336 <          THRCOF[ii] = 0.0;
334 >        std::pair<int,int> lm = std::make_pair(l, m1);
335 >        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
336 >          int m2 = m2Min[lm] + mmm;
337 >          int m3 = -m1-m2;
338 >          W[l] += w3j[lm][mmm] * QBar[lm] *
339 >            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
340          }
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 –        }
341        }
342        
343        W_hat[l] = W[l] / pow(Q2[l], 1.5);
# Line 286 | Line 346 | namespace oopse {
346      writeOrderParameter(Q, W_hat);    
347    }
348  
349 <  void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
349 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
350 >                                            std::vector<ComplexType> what) {
351  
352      for (int l = 0; l <= lMax_; l++) {
353        if (q[l] >= MinQ_ && q[l] < MaxQ_) {
# Line 302 | Line 363 | namespace oopse {
363        }
364      }
365  
366 +    for (int l = 0; l <= lMax_; l++) {
367 +      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
368 +        int wbin = (real(what[l]) - MinW_) / deltaW_;
369 +        W_histogram_[std::make_pair(wbin,l)] += 1;
370 +        Wcount_[l]++;      
371 +      } else {
372 +        sprintf( painCave.errMsg,
373 +                 "Re[w_hat] value outside reasonable range\n");
374 +        painCave.severity = OOPSE_ERROR;
375 +        painCave.isFatal = 1;
376 +        simError();  
377 +      }
378 +    }
379 +
380    }  
381  
382  
383 <  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
383 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
384 >                                               std::vector<ComplexType> What) {
385      
386 <    std::ofstream os(getOutputFileName().c_str());
387 <    
388 <    if (os.is_open()) {
386 >    std::ofstream osq((getOutputFileName() + "q").c_str());
387 >
388 >    if (osq.is_open()) {
389        
390 <      os << "# Bond Order Parameters\n";
391 <      os << "# selection: (" << selectionScript_ << ")\n";
390 >      osq << "# Bond Order Parameters\n";
391 >      osq << "# selection: (" << selectionScript_ << ")\n";
392 >      osq << "# \n";
393        for (int l = 0; l <= lMax_; l++) {
394 <        os << "# \n";
318 <        os << "# <Q_" << l << ">: " << Q[l] << "\n";
319 <        os << "# <W_" << l << ">: " << real(What[l]) << "\n";
394 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
395        }
396        // Normalize by number of frames and write it out:
397        for (int i = 0; i < nBins_; ++i) {
398          RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
399 <        os << Qval;
399 >        osq << Qval;
400          for (int l = 0; l <= lMax_; l++) {
401 <          os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
401 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
402 >            (RealType)Qcount_[l];
403          }
404 <        os << "\n";
404 >        osq << "\n";
405        }
406  
407 <      os.close();
407 >      osq.close();
408  
409      } else {
410        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
411 <              getOutputFileName().c_str());
411 >              (getOutputFileName() + "q").c_str());
412        painCave.isFatal = 1;
413        simError();  
414      }
415 +
416 +    std::ofstream osw((getOutputFileName() + "w").c_str());
417 +
418 +    if (osw.is_open()) {
419 +      osw << "# Bond Order Parameters\n";
420 +      osw << "# selection: (" << selectionScript_ << ")\n";
421 +      osw << "# \n";
422 +      for (int l = 0; l <= lMax_; l++) {
423 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
424 +      }
425 +      // Normalize by number of frames and write it out:
426 +      for (int i = 0; i < nBins_; ++i) {
427 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
428 +        osw << Wval;
429 +        for (int l = 0; l <= lMax_; l++) {
430 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
431 +            (RealType)Wcount_[l];
432 +        }
433 +        osw << "\n";
434 +      }
435 +
436 +      osw.close();
437 +    } else {
438 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
439 +              (getOutputFileName() + "w").c_str());
440 +      painCave.isFatal = 1;
441 +      simError();  
442 +    }
443 +      
444    }
445   }

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