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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 1042 by gezelter, Wed Sep 20 22:16:23 2006 UTC

# Line 51 | Line 51
51   #include "io/DumpReader.hpp"
52   #include "primitives/Molecule.hpp"
53   #include "utils/NumericConstant.hpp"
54 < #include "math/RealSphericalHarmonic.hpp"
54 > #include "math/SphericalHarmonic.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 100 | Line 108 | namespace oopse {
108      Molecule::RigidBodyIterator rbIter;
109      Molecule::AtomIterator ai;
110      StuntDouble* sd;
111 <    RealType theta;
111 >    RealType costheta;
112      RealType phi;
113      RealType r;
114      RealType dist;
115 <    std::map<int, RealType> QBar_lm;
115 >    std::map<int, ComplexType> QBar_lm;
116      RealType QSq_l;
117      RealType Q_l;
118      int nBonds;
119 <    RealSphericalHarmonic sphericalHarmonic;
119 >    SphericalHarmonic 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 168 | Line 180 | namespace oopse {
180              // Check to see if neighbor is in bond cutoff
181              
182              if (r < rCut_) {            
183 <              theta = atan2(vec.y(), vec.x());
184 <              phi = acos(vec.z()/r);
183 >              costheta = vec.z() / r;
184 >              phi = atan2(vec.y(), vec.x());
185 >              
186                for(int m = -lNumber_; m <= lNumber_; m++){
187                  sphericalHarmonic.setM(m);
188 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
188 >                QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
189                }
190                nBonds++;
191              }  
192            }
193          }
194          
195 <        // Normalize Qbar
195 >        // Normalize Qbar2
196          for (int m = -lNumber_;m <= lNumber_; m++){
197            QBar_lm[m] /= nBonds;
198          }
# Line 188 | Line 201 | namespace oopse {
201  
202          QSq_l = 0.0;
203          for (int m = -lNumber_; m <= lNumber_; m++){
204 <          QSq_l += pow(QBar_lm[m], 2);  
204 >          QSq_l += norm(QBar_lm[m]);
205          }
206          Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
207      
# Line 198 | Line 211 | namespace oopse {
211          double* THRCOF = new double[mSize_];
212          // Variables for Wigner routine
213          double l_ = (double)lNumber_;
214 <        double m2Min, m2Max;
214 >        double m1Pass, m2Min, m2Max;
215          int error, m1, m2, m3;
216 <        
217 <        W_l_ = 0.0;
216 >
217 >        ComplexType W_l;
218 >        ComplexType W_l_hat;
219 >        W_l = 0.0;
220          for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
221            // Zero work array
222 <          for (int ii = 0; ii < mSize_; ii+){
222 >          for (int ii = 0; ii < mSize_; ii++){
223              THRCOF[i] = 0.0;
224            }
225            // Get Wigner coefficients
226 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
226 >          m1Pass = (double)m1;
227 >          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
228            for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
229              m2 = floor(m2Min) + m_index - 1;
230              m3 = -m1-m2;
231 <            W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
231 >            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
232            }
233          }
234  
235 <        W_l_hat = W_l_ / pow(QSq_l, 1.5);
235 >        W_l_hat = W_l / pow(QSq_l, 1.5);
236  
237          // accumulate histogram data for Q_l and W_l_hat:
238  
239 <        collectHistogram(Q_l, W_l_hat);
239 >        collectHistogram(Q_l, real(W_l_hat));
240                  
241        }
242      }
243      
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 –    
244      writeOrderParameter();
245      
246    }
247  
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;
248  
249 <    for(int i = 0 ; i < histogram_.size(); ++i){
249 >  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
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;    
251 >    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
252 >      int qbin = (Q_l - MinQ_) / deltaQ_;
253 >      Q_histogram_[qbin] += 1;
254 >      Qcount_++;
255 >      sumQ_ += Q_l;
256 >      sumQ2_ += Q_l * Q_l;
257 >    } else {
258 >      sprintf( painCave.errMsg,
259 >               "Q_l value outside reasonable range\n");
260 >      painCave.severity = OOPSE_ERROR;
261 >      painCave.isFatal = 1;
262 >      simError();  
263      }
264  
265 <  }
266 <
267 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
268 <
269 <    if (Q_l < Max_Q) {
270 <      int whichBin = Q_l / deltaQ_;
271 <      Q_histogram_[whichBin] += 1;
265 >    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
266 >      int wbin = (W_l_hat - MinW_) / deltaW_;
267 >      W_histogram_[wbin] += 1;
268 >      Wcount_++;
269 >      sumW_  += W_l_hat;
270 >      sumW2_ += W_l_hat*W_l_hat;
271 >    } else {
272 >      sprintf( painCave.errMsg,
273 >               "W_l_hat value outside reasonable range\n");
274 >      painCave.severity = OOPSE_ERROR;
275 >      painCave.isFatal = 1;
276 >      simError();  
277      }
278 <    if (W_l_hat < Max_W) {
268 <      int whichBin = W_l_hat / deltaW_;
269 <      W_histogram_[whichBin] += 1;
270 <    }
271 <  }
272 <  
278 >  }  
279  
280    void BondOrderParameter::writeOrderParameter() {
281  
282 <    std::ofstream os(getOutputFileName().c_str());
277 <    os << "#Bond Order Parameter\n";
278 <    os << "#selection: (" << selectionScript_ << ")\n";
282 >    std::ofstream osq((getOutputFileName() + "q").c_str());
283  
284 <    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";
284 >    if (osq.is_open()) {
285  
286 +      RealType qAvg = sumQ_ / (RealType) Qcount_;
287 +      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
288 +      
289 +      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
290 +      osq << "# selection: (" << selectionScript_ << ")\n";
291 +      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
292 +      osq << "# std. dev.: " << qStdDev << "\n";
293 +      
294 +      // Normalize by number of frames and write it out:
295 +      for (int i = 0; i < Q_histogram_.size(); ++i) {
296 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
297 +        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
298 +      }
299 +      
300 +      osq.close();
301 +    } else {
302 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
303 +              (getOutputFileName() + "q").c_str());
304 +      painCave.isFatal = 1;
305 +      simError();  
306      }
288 –  }
307  
308 +    std::ofstream osw((getOutputFileName() + "w").c_str());
309  
310 +    if (osw.is_open()) {
311  
312 +      RealType wAvg = sumW_ / (RealType) Wcount_;
313 +      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
314 +      
315 +      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
316 +      osw << "# selection: (" << selectionScript_ << ")\n";
317 +      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
318 +      osw << "# std. dev.: " << wStdDev << "\n";
319 +      
320 +      // Normalize by number of frames and write it out:
321 +      for (int i = 0; i < W_histogram_.size(); ++i) {
322 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
323 +        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
324 +      }
325 +      
326 +      osw.close();
327 +    } else {
328 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
329 +              (getOutputFileName() + "w").c_str());
330 +      painCave.isFatal = 1;
331 +      simError();  
332 +    }
333 +  }
334   }

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