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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 1040 by gezelter, Tue Sep 19 21:20:15 2006 UTC vs.
Revision 1046 by gezelter, Thu Sep 21 20:43:17 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 <    deltaQ_ = 1.0 / nbins;
79 <    deltaW_ = 2.0 / nbins;
76 >    // Q can take values from 0 to 1
77  
78 +    MinQ_ = 0.0;
79 +    MaxQ_ = 3.0;
80 +    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81      Q_histogram_.resize(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_ = -0.18;
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 92 | Line 104 | namespace oopse {
104      Molecule* mol;
105      Atom* atom;
106      RigidBody* rb;
107 +    int myIndex;
108      SimInfo::MoleculeIterator mi;
109      Molecule::RigidBodyIterator rbIter;
110      Molecule::AtomIterator ai;
111      StuntDouble* sd;
112 <    RealType theta;
112 >    Vector3d vec;
113 >    RealType costheta;
114      RealType phi;
115      RealType r;
116      RealType dist;
117 <    std::map<int, RealType> QBar_lm;
117 >    std::map<int,ComplexType> QBar_lm;
118      RealType QSq_l;
119      RealType Q_l;
120 +    ComplexType W_l;
121 +    ComplexType W_l_hat;
122      int nBonds;
123 <    RealSphericalHarmonic sphericalHarmonic;
123 >    SphericalHarmonic sphericalHarmonic;
124      int i, j;
125 <  
125 >    // Make arrays for Wigner3jm
126 >    double* THRCOF = new double[mSize_];
127 >    // Variables for Wigner routine
128 >    double l_ = (double)lNumber_;
129 >    double m1Pass, m2Min, m2Max;
130 >    int error, m1, m2, m3;
131 >
132      // Set the l for the spherical harmonic, it doesn't change
133      sphericalHarmonic.setL(lNumber_);
134  
113 –
135      DumpReader reader(info_, dumpFilename_);    
136      int nFrames = reader.getNFrames();
137 +    frameCounter_ = 0;
138  
117 –
139      for (int istep = 0; istep < nFrames; istep += step_) {
140        reader.readFrame(istep);
141 +      frameCounter_++;
142        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
143        
144        if (evaluator_.isDynamic()) {
# Line 138 | Line 160 | namespace oopse {
160        for (sd = seleMan_.beginSelected(i); sd != NULL;
161             sd = seleMan_.nextSelected(i)) {
162  
163 +        myIndex = sd->getGlobalIndex();
164 +
165          // For this central atom, zero out nBonds and QBar_lm
166  
167          nBonds = 0;
# Line 153 | Line 177 | namespace oopse {
177            for (atom = mol->beginAtom(ai); atom != NULL;
178                 atom = mol->nextAtom(ai)) {
179  
180 +            if (atom->getGlobalIndex() != myIndex) {
181  
182 <            Vector3d vec = sd->getPos() - atom->getPos();      
183 <            currentSnapshot_->wrapVector(vec);
184 <            
185 <            // Calculate "bonds" and build Q_lm(r) where
186 <            //      Q_lm = Y_lm(theta(r),phi(r))                
187 <            // The spherical harmonics are wrt any arbitrary coordinate
188 <            // system, we choose standard spherical coordinates
189 <            
190 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
191 <            
192 <            // Check to see if neighbor is in bond cutoff
193 <            
194 <            if (r < rCut_) {            
195 <              theta = atan2(vec.y(), vec.x());
196 <              phi = acos(vec.z()/r);
197 <              for(int m = -lNumber_; m <= lNumber_; m++){
198 <                sphericalHarmonic.setM(m);
199 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
200 <              }
201 <              nBonds++;
202 <            }  
182 >              vec = sd->getPos() - atom->getPos();      
183 >              currentSnapshot_->wrapVector(vec);
184 >              
185 >              // Calculate "bonds" and build Q_lm(r) where
186 >              //      Q_lm = Y_lm(theta(r),phi(r))                
187 >              // The spherical harmonics are wrt any arbitrary coordinate
188 >              // system, we choose standard spherical coordinates
189 >              
190 >              r = vec.length();
191 >              
192 >              // Check to see if neighbor is in bond cutoff
193 >              
194 >              if (r < rCut_) {
195 >                costheta = vec.z() / r;
196 >                phi = atan2(vec.y(), vec.x());
197 >                
198 >                for(int m = -lNumber_; m <= lNumber_; m++){
199 >                  sphericalHarmonic.setM(m);
200 >                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
201 >                }
202 >                nBonds++;
203 >              }  
204 >            }
205            }
206          }
207          
208 <        // Normalize Qbar
208 >        // Normalize Qbar2
209          for (int m = -lNumber_;m <= lNumber_; m++){
210            QBar_lm[m] /= nBonds;
211          }
# Line 187 | Line 214 | namespace oopse {
214  
215          QSq_l = 0.0;
216          for (int m = -lNumber_; m <= lNumber_; m++){
217 <          QSq_l += pow(QBar_lm[m], 2);  
217 >          QSq_l += norm(QBar_lm[m]);
218          }
192 –        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
193 –    
194 –        // Find Third Order Invariant W_l
219  
220 <        // Make arrays for Wigner3jm
221 <        double* THRCOF = new double[mSize_];
198 <        // Variables for Wigner routine
199 <        double l_ = (double)lNumber_;
200 <        double m2Min, m2Max;
201 <        int error, m1, m2, m3;
220 >        Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
221 >                   (2.0*(RealType)lNumber_ + 1.0));
222  
223 <        RealType W_l;
224 <        RealType W_l_hat;
223 >        // Find Third Order Invariant W_l
224 >        
225          W_l = 0.0;
226          for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
227            // Zero work array
228            for (int ii = 0; ii < mSize_; ii++){
229 <            THRCOF[i] = 0.0;
229 >            THRCOF[ii] = 0.0;
230            }
231            // Get Wigner coefficients
232 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
233 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
234 <            m2 = floor(m2Min) + m_index - 1;
232 >          m1Pass = (double)m1;
233 >
234 >          Wigner3jm(&l_, &l_, &l_,
235 >                    &m1Pass, &m2Min, &m2Max,
236 >                    THRCOF, &mSize_, &error);
237 >
238 >          for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
239 >            m2 = (int)floor(m2Min) + mmm;
240              m3 = -m1-m2;
241 <            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
241 >            W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
242            }
243          }
244 <
244 >        
245          W_l_hat = W_l / pow(QSq_l, 1.5);
246 <
246 >        
247          // accumulate histogram data for Q_l and W_l_hat:
248  
249 <        collectHistogram(Q_l, W_l_hat);
249 >        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
250 >        collectHistogram(Q_l, real(W_l_hat));
251                  
252        }
253      }
254      
229 –    // Normalize by number of frames
230 –    for (int m = -lNumber_; m <= lNumber_; m++){
231 –      QBar_lm[m] /=  nFrames;  
232 –    }
233 –    
234 –    
235 –    
236 –    
237 –    
255      writeOrderParameter();
256      
257    }
258  
242 –  
243 –  void BondOrderParameter::processHistogram() {
244 –    
245 –    int nPairs = getNPairs();
246 –    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
247 –    RealType pairDensity = nPairs /volume * 2.0;
248 –    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
259  
260 <    for(int i = 0 ; i < histogram_.size(); ++i){
260 >  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
261  
262 <      RealType rLower = i * deltaR_;
263 <      RealType rUpper = rLower + deltaR_;
264 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
265 <      RealType nIdeal = volSlice * pairConstant;
266 <
267 <      avgGofr_[i] += histogram_[i] / nIdeal;    
262 >    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
263 >      int qbin = (Q_l - MinQ_) / deltaQ_;
264 >      Q_histogram_[qbin] += 1;
265 >      Qcount_++;
266 >      sumQ_ += Q_l;
267 >      sumQ2_ += Q_l * Q_l;
268 >    } else {
269 >      sprintf( painCave.errMsg,
270 >               "Q_l value outside reasonable range\n");
271 >      painCave.severity = OOPSE_ERROR;
272 >      painCave.isFatal = 1;
273 >      simError();  
274      }
275  
276 <  }
277 <
278 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
279 <
280 <    if (Q_l < MaxQ_) {
281 <      int whichBin = Q_l / deltaQ_;
282 <      Q_histogram_[whichBin] += 1;
276 >    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
277 >      int wbin = (W_l_hat - MinW_) / deltaW_;
278 >      W_histogram_[wbin] += 1;
279 >      Wcount_++;
280 >      sumW_  += W_l_hat;
281 >      sumW2_ += W_l_hat*W_l_hat;
282 >    } else {
283 >      sprintf( painCave.errMsg,
284 >               "W_l_hat value outside reasonable range\n");
285 >      painCave.severity = OOPSE_ERROR;
286 >      painCave.isFatal = 1;
287 >      simError();  
288      }
289 <    if (W_l_hat < MaxW_) {
269 <      int whichBin = W_l_hat / deltaW_;
270 <      W_histogram_[whichBin] += 1;
271 <    }
272 <  }
273 <  
289 >  }  
290  
291    void BondOrderParameter::writeOrderParameter() {
292  
293 <    std::ofstream os(getOutputFileName().c_str());
278 <    os << "#Bond Order Parameter\n";
279 <    os << "#selection: (" << selectionScript_ << ")\n";
293 >    std::ofstream osq((getOutputFileName() + "q").c_str());
294  
295 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
282 <      os <<  orderParams_[i].p2 << "\t"
283 <         <<  orderParams_[i].director[0] << "\t"
284 <         <<  orderParams_[i].director[1] << "\t"
285 <         <<  orderParams_[i].director[2] << "\t"
286 <         <<  orderParams_[i].angle << "\n";
295 >    if (osq.is_open()) {
296  
297 +      RealType qAvg = sumQ_ / (RealType) Qcount_;
298 +      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
299 +      
300 +      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
301 +      osq << "# selection: (" << selectionScript_ << ")\n";
302 +      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
303 +      osq << "# std. dev.: " << qStdDev << "\n";
304 +      
305 +      // Normalize by number of frames and write it out:
306 +      for (int i = 0; i < Q_histogram_.size(); ++i) {
307 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
308 +        osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
309 +      }
310 +      
311 +      osq.close();
312 +    } else {
313 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
314 +              (getOutputFileName() + "q").c_str());
315 +      painCave.isFatal = 1;
316 +      simError();  
317      }
289 –  }
318  
319 +    std::ofstream osw((getOutputFileName() + "w").c_str());
320  
321 +    if (osw.is_open()) {
322  
323 +      RealType wAvg = sumW_ / (RealType) Wcount_;
324 +      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
325 +      
326 +      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
327 +      osw << "# selection: (" << selectionScript_ << ")\n";
328 +      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
329 +      osw << "# std. dev.: " << wStdDev << "\n";
330 +      
331 +      // Normalize by number of frames and write it out:
332 +      for (int i = 0; i < W_histogram_.size(); ++i) {
333 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
334 +        osw << Wval << "\t" << (RealType)W_histogram_[i] / (RealType)Wcount_ << "\n";
335 +      }
336 +      
337 +      osw.close();
338 +    } else {
339 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
340 +              (getOutputFileName() + "w").c_str());
341 +      painCave.isFatal = 1;
342 +      simError();  
343 +    }
344 +  }
345   }

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