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root/OpenMD/trunk/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1041 by gezelter, Wed Sep 20 20:13:40 2006 UTC

# Line 52 | Line 52
52   #include "primitives/Molecule.hpp"
53   #include "utils/NumericConstant.hpp"
54   #include "math/RealSphericalHarmonic.hpp"
55 +
56   namespace oopse {
57  
57 –
58    BondOrderParameter::BondOrderParameter(SimInfo* info,
59                                           const std::string& filename,
60                                           const std::string& sele,
61 <                                         double rCut, int lNumber, int nbins)
62 <    : StaticAnalyser(info, filename), selectionScript_(sele),
63 <      evaluator_(info), seleMan_(info){
61 >                                         double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62      
63 <    setOutputName(getPrefix(filename) + ".obo");
63 >    setOutputName(getPrefix(filename) + ".bo");
64  
65      evaluator_.loadScriptString(sele);
66      if (!evaluator_.isDynamic()) {
# Line 75 | Line 73 | namespace oopse {
73      rCut_ = rCut;
74      mSize_ = 2*lNumber_+1;    
75  
76 <    // Set the l for the spherical harmonic, it doesn't change
76 >    // Q can take values from 0 to 1
77  
78 <    sphericalHarmonic.setL(lNumber_);
78 >    MinQ_ = 0.0;
79 >    MaxQ_ = 1.0;
80 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81 >    Q_histogram_.resize(nbins);
82  
83 <    delta_Q = 1.0 / nbins;
84 <    delta_W = 2.0 / nbins;
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 <    Q_histogram_.resize(nbins);
86 >    MinW_ = -0.18;
87 >    MaxW_ = 0.18;
88 >    deltaW_ = (MaxW_ - MinW_) / nbins;
89      W_histogram_.resize(nbins);
90  
91    }
92  
93 +  BondOrderParameter::~BondOrderParameter() {
94 +    Q_histogram_.clear();
95 +    W_histogram_.clear();
96 +  }
97 +
98    void BondOrderParameter::initalizeHistogram() {
99      std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
100      std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
# Line 111 | Line 119 | namespace oopse {
119      RealSphericalHarmonic sphericalHarmonic;
120      int i, j;
121    
122 <  
122 >    // Set the l for the spherical harmonic, it doesn't change
123 >    sphericalHarmonic.setL(lNumber_);
124 >
125 >
126      DumpReader reader(info_, dumpFilename_);    
127      int nFrames = reader.getNFrames();
128 +    frameCounter_ = 0;
129  
118 –
130      for (int istep = 0; istep < nFrames; istep += step_) {
131        reader.readFrame(istep);
132 +      frameCounter_++;
133        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
134        
135        if (evaluator_.isDynamic()) {
# Line 198 | Line 210 | namespace oopse {
210          double* THRCOF = new double[mSize_];
211          // Variables for Wigner routine
212          double l_ = (double)lNumber_;
213 <        double m2Min, m2Max;
213 >        double m1Pass, m2Min, m2Max;
214          int error, m1, m2, m3;
215 <        
216 <        W_l_ = 0.0;
215 >
216 >        RealType W_l;
217 >        RealType W_l_hat;
218 >        W_l = 0.0;
219          for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
220            // Zero work array
221 <          for (int ii = 0; ii < mSize_; ii+){
221 >          for (int ii = 0; ii < mSize_; ii++){
222              THRCOF[i] = 0.0;
223            }
224            // Get Wigner coefficients
225 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
225 >          m1Pass = (double)m1;
226 >          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
227            for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
228              m2 = floor(m2Min) + m_index - 1;
229              m3 = -m1-m2;
230 <            W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
230 >            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
231            }
232          }
233  
234 <        W_l_hat = W_l_ / pow(QSq_l, 1.5);
234 >        W_l_hat = W_l / pow(QSq_l, 1.5);
235  
236          // accumulate histogram data for Q_l and W_l_hat:
237  
# Line 225 | Line 240 | namespace oopse {
240        }
241      }
242      
228 –    // Normalize by number of frames
229 –    for (int m = -lNumber_; m <= lNumber_; m++){
230 –      QBar_lm[m] /=  nFrames;  
231 –    }
232 –    
233 –    
234 –    
235 –    
236 –    
243      writeOrderParameter();
244      
245    }
246  
241 –  
242 –  void BondOrderParameter::processHistogram() {
243 –    
244 –    int nPairs = getNPairs();
245 –    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
246 –    RealType pairDensity = nPairs /volume * 2.0;
247 –    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
247  
249 –    for(int i = 0 ; i < histogram_.size(); ++i){
250 –
251 –      RealType rLower = i * deltaR_;
252 –      RealType rUpper = rLower + deltaR_;
253 –      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
254 –      RealType nIdeal = volSlice * pairConstant;
255 –
256 –      avgGofr_[i] += histogram_[i] / nIdeal;    
257 –    }
258 –
259 –  }
260 –
248    void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
249  
250 <    if (Q_l < Max_Q) {
251 <      int whichBin = Q_l / deltaQ_;
252 <      Q_histogram_[whichBin] += 1;
253 <    }
254 <    if (W_l_hat < Max_W) {
255 <      int whichBin = W_l_hat / deltaW_;
256 <      W_histogram_[whichBin] += 1;
250 >    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
251 >      int qbin = (Q_l - MinQ_) / deltaQ_;
252 >      Q_histogram_[qbin] += 1;
253 >      Qcount_++;
254 >      sumQ_ += Q_l;
255 >      sumQ2_ += Q_l * Q_l;
256 >    } else {
257 >      sprintf( painCave.errMsg,
258 >               "Q_l value outside reasonable range\n");
259 >      painCave.severity = OOPSE_ERROR;
260 >      painCave.isFatal = 1;
261 >      simError();  
262      }
271 –  }
272 –  
263  
264 +    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
265 +      int wbin = (W_l_hat - MinW_) / deltaW_;
266 +      W_histogram_[wbin] += 1;
267 +      Wcount_++;
268 +      sumW_  += W_l_hat;
269 +      sumW2_ += W_l_hat*W_l_hat;
270 +    } else {
271 +      sprintf( painCave.errMsg,
272 +               "W_l_hat value outside reasonable range\n");
273 +      painCave.severity = OOPSE_ERROR;
274 +      painCave.isFatal = 1;
275 +      simError();  
276 +    }
277 +  }  
278 +
279    void BondOrderParameter::writeOrderParameter() {
280  
281 <    std::ofstream os(getOutputFileName().c_str());
277 <    os << "#Bond Order Parameter\n";
278 <    os << "#selection: (" << selectionScript_ << ")\n";
281 >    std::ofstream osq((getOutputFileName() + "q").c_str());
282  
283 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
281 <      os <<  orderParams_[i].p2 << "\t"
282 <         <<  orderParams_[i].director[0] << "\t"
283 <         <<  orderParams_[i].director[1] << "\t"
284 <         <<  orderParams_[i].director[2] << "\t"
285 <         <<  orderParams_[i].angle << "\n";
283 >    if (osq.is_open()) {
284  
285 +      RealType qAvg = sumQ_ / (RealType) Qcount_;
286 +      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
287 +      
288 +      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
289 +      osq << "# selection: (" << selectionScript_ << ")\n";
290 +      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
291 +      osq << "# std. dev.: " << qStdDev << "\n";
292 +      
293 +      // Normalize by number of frames and write it out:
294 +      for (int i = 0; i < Q_histogram_.size(); ++i) {
295 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
296 +        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
297 +      }
298 +      
299 +      osq.close();
300 +    } else {
301 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
302 +              (getOutputFileName() + "q").c_str());
303 +      painCave.isFatal = 1;
304 +      simError();  
305      }
288 –  }
306  
307 +    std::ofstream osw((getOutputFileName() + "w").c_str());
308  
309 +    if (osw.is_open()) {
310  
311 +      RealType wAvg = sumW_ / (RealType) Wcount_;
312 +      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
313 +      
314 +      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
315 +      osw << "# selection: (" << selectionScript_ << ")\n";
316 +      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
317 +      osw << "# std. dev.: " << wStdDev << "\n";
318 +      
319 +      // Normalize by number of frames and write it out:
320 +      for (int i = 0; i < W_histogram_.size(); ++i) {
321 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
322 +        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
323 +      }
324 +      
325 +      osw.close();
326 +    } else {
327 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
328 +              (getOutputFileName() + "w").c_str());
329 +      painCave.isFatal = 1;
330 +      simError();  
331 +    }
332 +  }
333   }

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