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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 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"
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_ = -1.1;
87 +    MaxW_ = 1.1;
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 +    Nbonds = 0;
190 +
191      for (int istep = 0; istep < nFrames; istep += step_) {
192        reader.readFrame(istep);
193        frameCounter_++;
# Line 130 | Line 205 | namespace oopse {
205               rb = mol->nextRigidBody(rbIter)) {
206            rb->updateAtoms();
207          }        
208 <      }      
209 <      
135 <      nBonds = 0;
136 <      
137 <      for (int m = -lNumber_; m <= lNumber_; m++) {
138 <        QBar_lm[m] = 0.0;
139 <      }
140 <      
208 >      }          
209 >            
210        // outer loop is over the selected StuntDoubles:
211  
212        for (sd = seleMan_.beginSelected(i); sd != NULL;
213             sd = seleMan_.nextSelected(i)) {
214  
215          myIndex = sd->getGlobalIndex();
216 +        nBonds = 0;
217          
218 +        for (int l = 0; l <= lMax_; l++) {
219 +          for (int m = -l; m <= l; m++) {
220 +            q[std::make_pair(l,m)] = 0.0;
221 +          }
222 +        }
223 +        
224          // inner loop is over all other atoms in the system:
225          
226          for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 155 | 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 169 | Line 247 | namespace oopse {
247                if (r < rCut_) {
248                  costheta = vec.z() / r;
249                  phi = atan2(vec.y(), vec.x());
250 <                
251 <                for(int m = -lNumber_; m <= lNumber_; m++){
252 <                  sphericalHarmonic.setM(m);
253 <                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
250 >
251 >                for (int l = 0; l <= lMax_; l++) {
252 >                  sphericalHarmonic.setL(l);
253 >                  for(int m = -l; m <= l; m++){
254 >                    sphericalHarmonic.setM(m);
255 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256 >                  }
257                  }
258                  nBonds++;
259                }  
260              }
261            }
262          }
263 <      }      
264 <    }
263 >        
264 >        
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 >        }
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)] += (RealType)nBonds*q[std::make_pair(l,m)];
297 +          }
298 +        }
299 +      }
300 +    }
301 +      
302      // Normalize Qbar2
303 <    for (int m = -lNumber_;m <= lNumber_; m++){
304 <      QBar_lm[m] /= nBonds;
303 >    for (int l = 0; l <= lMax_; l++) {
304 >      for (int m = -l; m <= l; m++){
305 >        QBar[std::make_pair(l,m)] /= Nbonds;
306 >      }
307      }
308      
309      // Find second order invariant Q_l
310      
311 <    QSq_l = 0.0;
312 <    for (int m = -lNumber_; m <= lNumber_; m++){
313 <      QSq_l += norm(QBar_lm[m]);
311 >    for (int l = 0; l <= lMax_; l++) {
312 >      Q2[l] = 0.0;
313 >      for (int m = -l; m <= l; m++){
314 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
315 >      }
316 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317      }
318      
197 –    std::cout << "qsl = " << QSq_l << "\n";
198 –    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
199 –    
319      // Find Third Order Invariant W_l
320      
321 <    W_l = 0.0;
322 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
323 <      // Zero work array
324 <      for (int ii = 0; ii < mSize_; ii++){
325 <        THRCOF[ii] = 0.0;
321 >    for (int l = 0; l <= lMax_; l++) {
322 >      W[l] = 0.0;
323 >      for (int m1 = -l; m1 <= l; m1++) {
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 >        }
331        }
208 –      // Get Wigner coefficients
209 –      m1Pass = (double)m1;
332        
333 <      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 <      }
333 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
334      }
335      
336 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
223 <    
224 <    writeOrderParameter(Q_l, real(W_l_hat));    
336 >    writeOrderParameter(Q, W_hat);    
337    }
338  
339 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340 +                                            std::vector<ComplexType> what) {
341  
342 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
342 >    for (int l = 0; l <= lMax_; l++) {
343 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344 >        int qbin = (q[l] - MinQ_) / deltaQ_;
345 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
346 >        Qcount_[l]++;      
347 >      } else {
348 >        sprintf( painCave.errMsg,
349 >                 "q_l value outside reasonable range\n");
350 >        painCave.severity = OOPSE_ERROR;
351 >        painCave.isFatal = 1;
352 >        simError();  
353 >      }
354 >    }
355  
356 <    std::ofstream os(getOutputFileName().c_str());
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 <    if (os.is_open()) {
370 >  }  
371 >
372 >
373 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374 >                                               std::vector<ComplexType> What) {
375 >    
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";
382 <      os << "# \n";
383 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
384 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
385 <      os.close();
380 >      osq << "# Bond Order Parameters\n";
381 >      osq << "# selection: (" << selectionScript_ << ")\n";
382 >      osq << "# \n";
383 >      for (int l = 0; l <= lMax_; l++) {
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 >        osq << Qval;
390 >        for (int l = 0; l <= lMax_; l++) {
391  
392 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393 +        }
394 +        osq << "\n";
395 +      }
396 +
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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