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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 3026 by gezelter, Tue Sep 26 16:08:44 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 1.18 2006-09-26 16:08:44 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 223 | Line 267 | namespace oopse {
267            q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
268            q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
269          }
270 <        collectHistogram(q_l);
270 >
271 >        // Find second order invariant Q_l
272          
273 +        for (int l = 0; l <= lMax_; l++) {
274 +          q2[l] = 0.0;
275 +          for (int m = -l; m <= l; m++){
276 +            q2[l] += norm(q[std::make_pair(l,m)]);
277 +          }
278 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
279 +                        (RealType)(2*l + 1))/(RealType)nBonds;
280 +        }
281 +
282 +        // Find Third Order Invariant W_l
283 +    
284 +        for (int l = 0; l <= lMax_; l++) {
285 +          w[l] = 0.0;
286 +          for (int m1 = -l; m1 <= l; m1++) {
287 +            std::pair<int,int> lm = std::make_pair(l, m1);
288 +            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
289 +              int m2 = m2Min[lm] + mmm;
290 +              int m3 = -m1-m2;
291 +              w[l] += w3j[lm][mmm] * q[lm] *
292 +                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
293 +            }
294 +          }
295 +          
296 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
297 +        }
298 +
299 +        collectHistogram(q_l, w_hat);
300 +        
301          Nbonds += nBonds;
302          for (int l = 0; l <= lMax_;  l++) {
303            for (int m = -l; m <= l; m++) {
# Line 251 | Line 324 | namespace oopse {
324        Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
325      }
326      
254 –
255 –    
327      // Find Third Order Invariant W_l
328      
329      for (int l = 0; l <= lMax_; l++) {
330        W[l] = 0.0;
260 –      lPass = (double)l;
331        for (int m1 = -l; m1 <= l; m1++) {
332 <        // Zero work array
333 <        for (int ii = 0; ii < 2*l + 1; ii++){
334 <          THRCOF[ii] = 0.0;
332 >        std::pair<int,int> lm = std::make_pair(l, m1);
333 >        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
334 >          int m2 = m2Min[lm] + mmm;
335 >          int m3 = -m1-m2;
336 >          W[l] += w3j[lm][mmm] * QBar[lm] *
337 >            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
338          }
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 –        }
339        }
340        
341        W_hat[l] = W[l] / pow(Q2[l], 1.5);
# Line 286 | Line 344 | namespace oopse {
344      writeOrderParameter(Q, W_hat);    
345    }
346  
347 <  void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
347 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
348 >                                            std::vector<ComplexType> what) {
349  
350      for (int l = 0; l <= lMax_; l++) {
351        if (q[l] >= MinQ_ && q[l] < MaxQ_) {
# Line 302 | Line 361 | namespace oopse {
361        }
362      }
363  
364 +    for (int l = 0; l <= lMax_; l++) {
365 +      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
366 +        int wbin = (real(what[l]) - MinW_) / deltaW_;
367 +        W_histogram_[std::make_pair(wbin,l)] += 1;
368 +        Wcount_[l]++;      
369 +      } else {
370 +        sprintf( painCave.errMsg,
371 +                 "Re[w_hat] value outside reasonable range\n");
372 +        painCave.severity = OOPSE_ERROR;
373 +        painCave.isFatal = 1;
374 +        simError();  
375 +      }
376 +    }
377 +
378    }  
379  
380  
381 <  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
381 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
382 >                                               std::vector<ComplexType> What) {
383      
384 <    std::ofstream os(getOutputFileName().c_str());
385 <    
386 <    if (os.is_open()) {
384 >    std::ofstream osq((getOutputFileName() + "q").c_str());
385 >
386 >    if (osq.is_open()) {
387        
388 <      os << "# Bond Order Parameters\n";
389 <      os << "# selection: (" << selectionScript_ << ")\n";
388 >      osq << "# Bond Order Parameters\n";
389 >      osq << "# selection: (" << selectionScript_ << ")\n";
390 >      osq << "# \n";
391        for (int l = 0; l <= lMax_; l++) {
392 <        os << "# \n";
318 <        os << "# <Q_" << l << ">: " << Q[l] << "\n";
319 <        os << "# <W_" << l << ">: " << real(What[l]) << "\n";
392 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
393        }
394        // Normalize by number of frames and write it out:
395        for (int i = 0; i < nBins_; ++i) {
396          RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
397 <        os << Qval;
397 >        osq << Qval;
398          for (int l = 0; l <= lMax_; l++) {
399 <          os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
399 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
400 >            (RealType)Qcount_[l];
401          }
402 <        os << "\n";
402 >        osq << "\n";
403        }
404  
405 <      os.close();
405 >      osq.close();
406  
407      } else {
408        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
409 <              getOutputFileName().c_str());
409 >              (getOutputFileName() + "q").c_str());
410        painCave.isFatal = 1;
411        simError();  
412      }
413 +
414 +    std::ofstream osw((getOutputFileName() + "w").c_str());
415 +
416 +    if (osw.is_open()) {
417 +      osw << "# Bond Order Parameters\n";
418 +      osw << "# selection: (" << selectionScript_ << ")\n";
419 +      osw << "# \n";
420 +      for (int l = 0; l <= lMax_; l++) {
421 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
422 +      }
423 +      // Normalize by number of frames and write it out:
424 +      for (int i = 0; i < nBins_; ++i) {
425 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
426 +        osw << Wval;
427 +        for (int l = 0; l <= lMax_; l++) {
428 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
429 +            (RealType)Wcount_[l];
430 +        }
431 +        osw << "\n";
432 +      }
433 +
434 +      osw.close();
435 +    } else {
436 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
437 +              (getOutputFileName() + "w").c_str());
438 +      painCave.isFatal = 1;
439 +      simError();  
440 +    }
441 +      
442    }
443   }

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