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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3015 by gezelter, Thu Sep 21 21:47:17 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"
52   #include "io/DumpReader.hpp"
53   #include "primitives/Molecule.hpp"
54   #include "utils/NumericConstant.hpp"
54 – #include "math/SphericalHarmonic.hpp"
55  
56   namespace oopse {
57  
58    BondOrderParameter::BondOrderParameter(SimInfo* info,
59                                           const std::string& filename,
60                                           const std::string& sele,
61 <                                         double rCut, int lNumber, 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 69 | Line 69 | namespace oopse {
69  
70      // Set up cutoff radius and order of the Legendre Polynomial:
71  
72 –    lNumber_ = lNumber;
72      rCut_ = rCut;
73 <    mSize_ = 2*lNumber_+1;    
74 <  }
73 >    nBins_ = nbins;
74 >    Qcount_.resize(lMax_+1);
75 >    Wcount_.resize(lMax_+1);
76  
77 +    // Q can take values from 0 to 1
78 +
79 +    MinQ_ = 0.0;
80 +    MaxQ_ = 1.1;
81 +    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
82 +
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_ = -0.25;
87 +    MaxW_ = 0.25;
88 +    deltaW_ = (MaxW_ - MinW_) / nbins;
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 +  
139 +  void BondOrderParameter::initalizeHistogram() {
140 +    for (int bin = 0; bin < nBins_; bin++) {
141 +      for (int l = 0; l <= lMax_; l++) {
142 +        Q_histogram_[std::make_pair(bin,l)] = 0;
143 +        W_histogram_[std::make_pair(bin,l)] = 0;
144 +      }
145 +    }
146 +  }
147  
148    void BondOrderParameter::process() {
149      Molecule* mol;
# Line 91 | Line 159 | namespace oopse {
159      RealType phi;
160      RealType r;
161      RealType dist;
162 <    std::map<int,ComplexType> QBar_lm;
163 <    RealType QSq_l;
164 <    RealType Q_l;
165 <    ComplexType W_l;
166 <    ComplexType W_l_hat;
167 <    int nBonds;
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;
170 >    std::vector<ComplexType> W;
171 >    std::vector<ComplexType> W_hat;
172 >    int nBonds, Nbonds;
173      SphericalHarmonic sphericalHarmonic;
174      int i, j;
102 –    // Make arrays for Wigner3jm
103 –    double* THRCOF = new double[mSize_];
104 –    // Variables for Wigner routine
105 –    double l_ = (double)lNumber_;
106 –    double m1Pass, m2Min, m2Max;
107 –    int error, m1, m2, m3;
175  
109 –    // Set the l for the spherical harmonic, it doesn't change
110 –    sphericalHarmonic.setL(lNumber_);
111 –
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 +
190      for (int istep = 0; istep < nFrames; istep += step_) {
191        reader.readFrame(istep);
192        frameCounter_++;
# Line 130 | Line 204 | namespace oopse {
204               rb = mol->nextRigidBody(rbIter)) {
205            rb->updateAtoms();
206          }        
207 <      }      
208 <      
135 <      nBonds = 0;
136 <      
137 <      for (int m = -lNumber_; m <= lNumber_; m++) {
138 <        QBar_lm[m] = 0.0;
139 <      }
140 <      
207 >      }          
208 >            
209        // outer loop is over the selected StuntDoubles:
210  
211        for (sd = seleMan_.beginSelected(i); sd != NULL;
212             sd = seleMan_.nextSelected(i)) {
213  
214          myIndex = sd->getGlobalIndex();
215 +        nBonds = 0;
216          
217 +        for (int l = 0; l <= lMax_; l++) {
218 +          for (int m = -l; m <= l; m++) {
219 +            q[std::make_pair(l,m)] = 0.0;
220 +          }
221 +        }
222 +        
223          // inner loop is over all other atoms in the system:
224          
225          for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 169 | Line 244 | namespace oopse {
244                if (r < rCut_) {
245                  costheta = vec.z() / r;
246                  phi = atan2(vec.y(), vec.x());
247 <                
248 <                for(int m = -lNumber_; m <= lNumber_; m++){
249 <                  sphericalHarmonic.setM(m);
250 <                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
247 >
248 >                for (int l = 0; l <= lMax_; l++) {
249 >                  sphericalHarmonic.setL(l);
250 >                  for(int m = -l; m <= l; m++){
251 >                    sphericalHarmonic.setM(m);
252 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
253 >                  }
254                  }
255                  nBonds++;
256                }  
257              }
258            }
259          }
260 <      }      
261 <    }
260 >        
261 >        
262 >        for (int l = 0; l <= lMax_; l++) {        
263 >          q_l[l] = 0.0;
264 >          for(int m = -l; m <= l; m++) {
265 >            q_l[l] += norm(q[std::make_pair(l,m)]);
266 >          }    
267 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
268 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
269 >        }
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++) {
304 +            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
305 +          }
306 +        }
307 +      }
308 +    }
309 +      
310      // Normalize Qbar2
311 <    for (int m = -lNumber_;m <= lNumber_; m++){
312 <      QBar_lm[m] /= nBonds;
311 >    for (int l = 0; l <= lMax_; l++) {
312 >      for (int m = -l; m <= l; m++){
313 >        QBar[std::make_pair(l,m)] /= Nbonds;
314 >      }
315      }
316      
317      // Find second order invariant Q_l
318      
319 <    QSq_l = 0.0;
320 <    for (int m = -lNumber_; m <= lNumber_; m++){
321 <      QSq_l += norm(QBar_lm[m]);
319 >    for (int l = 0; l <= lMax_; l++) {
320 >      Q2[l] = 0.0;
321 >      for (int m = -l; m <= l; m++){
322 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
323 >      }
324 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
325      }
326      
197 –    std::cout << "qsl = " << QSq_l << "\n";
198 –    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
199 –    
327      // Find Third Order Invariant W_l
328      
329 <    W_l = 0.0;
330 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
331 <      // Zero work array
332 <      for (int ii = 0; ii < mSize_; ii++){
333 <        THRCOF[ii] = 0.0;
329 >    for (int l = 0; l <= lMax_; l++) {
330 >      W[l] = 0.0;
331 >      for (int m1 = -l; m1 <= l; m1++) {
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 >        }
339        }
208 –      // Get Wigner coefficients
209 –      m1Pass = (double)m1;
340        
341 <      Wigner3jm(&l_, &l_, &l_,
212 <                &m1Pass, &m2Min, &m2Max,
213 <                THRCOF, &mSize_, &error);
214 <      
215 <      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
216 <        m2 = (int)floor(m2Min) + mmm;
217 <        m3 = -m1-m2;
218 <        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
219 <      }
341 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
342      }
343      
344 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
223 <    
224 <    writeOrderParameter(Q_l, real(W_l_hat));    
344 >    writeOrderParameter(Q, W_hat);    
345    }
346  
347 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
348 +                                            std::vector<ComplexType> what) {
349  
350 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
350 >    for (int l = 0; l <= lMax_; l++) {
351 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
352 >        int qbin = (q[l] - MinQ_) / deltaQ_;
353 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
354 >        Qcount_[l]++;      
355 >      } else {
356 >        sprintf( painCave.errMsg,
357 >                 "q_l value outside reasonable range\n");
358 >        painCave.severity = OOPSE_ERROR;
359 >        painCave.isFatal = 1;
360 >        simError();  
361 >      }
362 >    }
363  
364 <    std::ofstream os(getOutputFileName().c_str());
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 <    if (os.is_open()) {
378 >  }  
379 >
380 >
381 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
382 >                                               std::vector<ComplexType> What) {
383 >    
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";
390 <      os << "# \n";
391 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
392 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
393 <      os.close();
388 >      osq << "# Bond Order Parameters\n";
389 >      osq << "# selection: (" << selectionScript_ << ")\n";
390 >      osq << "# \n";
391 >      for (int l = 0; l <= lMax_; l++) {
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 >        osq << Qval;
398 >        for (int l = 0; l <= lMax_; l++) {
399 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
400 >            (RealType)Qcount_[l];
401 >        }
402 >        osq << "\n";
403 >      }
404  
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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