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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 1044 by gezelter, Thu Sep 21 18:04:52 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 96 | 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 <  
126 <  
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 >
135      DumpReader reader(info_, dumpFilename_);    
136      int nFrames = reader.getNFrames();
137 +    frameCounter_ = 0;
138  
118 –
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 139 | 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 154 | 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 +          std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
212          }
213  
214          // Find second order invariant Q_l
215  
216          QSq_l = 0.0;
217          for (int m = -lNumber_; m <= lNumber_; m++){
218 <          QSq_l += pow(QBar_lm[m], 2);  
218 >          QSq_l += norm(QBar_lm[m]);
219          }
220 <        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
221 <    
222 <        // Find Third Order Invariant W_l
220 >        std::cout << "qsq_l = " << QSq_l << "\n";
221 >        Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
222 >                   (2.0*(RealType)lNumber_ + 1.0));
223  
224 <        // Make arrays for Wigner3jm
198 <        double* THRCOF = new double[mSize_];
199 <        // Variables for Wigner routine
200 <        double l_ = (double)lNumber_;
201 <        double m2Min, m2Max;
202 <        int error, m1, m2, m3;
224 >        // Find Third Order Invariant W_l
225          
226 <        W_l_ = 0.0;
226 >        W_l = 0.0;
227          for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
228            // Zero work array
229 <          for (int ii = 0; ii < mSize_; ii+){
229 >          for (int ii = 0; ii < mSize_; ii++){
230              THRCOF[i] = 0.0;
231            }
232            // Get Wigner coefficients
233 <          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
234 <          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
233 >          m1Pass = (double)m1;
234 >          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
235 >          for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
236              m2 = floor(m2Min) + m_index - 1;
237              m3 = -m1-m2;
238 <            W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
238 >            W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3];
239            }
240          }
241 <
242 <        W_l_hat = W_l_ / pow(QSq_l, 1.5);
243 <
241 >        
242 >        W_l_hat = W_l / pow(QSq_l, 1.5);
243 >        
244          // accumulate histogram data for Q_l and W_l_hat:
245  
246 <        collectHistogram(Q_l, W_l_hat);
246 >        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
247 >        collectHistogram(Q_l, real(W_l_hat));
248                  
249        }
250      }
251      
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 –    
252      writeOrderParameter();
253      
254    }
255  
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;
256  
257 <    for(int i = 0 ; i < histogram_.size(); ++i){
257 >  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
258  
259 <      RealType rLower = i * deltaR_;
260 <      RealType rUpper = rLower + deltaR_;
261 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
262 <      RealType nIdeal = volSlice * pairConstant;
263 <
264 <      avgGofr_[i] += histogram_[i] / nIdeal;    
259 >    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
260 >      int qbin = (Q_l - MinQ_) / deltaQ_;
261 >      Q_histogram_[qbin] += 1;
262 >      Qcount_++;
263 >      sumQ_ += Q_l;
264 >      sumQ2_ += Q_l * Q_l;
265 >    } else {
266 >      sprintf( painCave.errMsg,
267 >               "Q_l value outside reasonable range\n");
268 >      painCave.severity = OOPSE_ERROR;
269 >      painCave.isFatal = 1;
270 >      simError();  
271      }
272  
273 <  }
274 <
275 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
276 <
277 <    if (Q_l < Max_Q) {
278 <      int whichBin = Q_l / deltaQ_;
279 <      Q_histogram_[whichBin] += 1;
273 >    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
274 >      int wbin = (W_l_hat - MinW_) / deltaW_;
275 >      W_histogram_[wbin] += 1;
276 >      Wcount_++;
277 >      sumW_  += W_l_hat;
278 >      sumW2_ += W_l_hat*W_l_hat;
279 >    } else {
280 >      sprintf( painCave.errMsg,
281 >               "W_l_hat value outside reasonable range\n");
282 >      painCave.severity = OOPSE_ERROR;
283 >      painCave.isFatal = 1;
284 >      simError();  
285      }
286 <    if (W_l_hat < Max_W) {
268 <      int whichBin = W_l_hat / deltaW_;
269 <      W_histogram_[whichBin] += 1;
270 <    }
271 <  }
272 <  
286 >  }  
287  
288    void BondOrderParameter::writeOrderParameter() {
289  
290 <    std::ofstream os(getOutputFileName().c_str());
277 <    os << "#Bond Order Parameter\n";
278 <    os << "#selection: (" << selectionScript_ << ")\n";
290 >    std::ofstream osq((getOutputFileName() + "q").c_str());
291  
292 <    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";
292 >    if (osq.is_open()) {
293  
294 +      RealType qAvg = sumQ_ / (RealType) Qcount_;
295 +      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
296 +      
297 +      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
298 +      osq << "# selection: (" << selectionScript_ << ")\n";
299 +      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
300 +      osq << "# std. dev.: " << qStdDev << "\n";
301 +      
302 +      // Normalize by number of frames and write it out:
303 +      for (int i = 0; i < Q_histogram_.size(); ++i) {
304 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
305 +        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
306 +      }
307 +      
308 +      osq.close();
309 +    } else {
310 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
311 +              (getOutputFileName() + "q").c_str());
312 +      painCave.isFatal = 1;
313 +      simError();  
314      }
288 –  }
315  
316 +    std::ofstream osw((getOutputFileName() + "w").c_str());
317  
318 +    if (osw.is_open()) {
319  
320 +      RealType wAvg = sumW_ / (RealType) Wcount_;
321 +      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
322 +      
323 +      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
324 +      osw << "# selection: (" << selectionScript_ << ")\n";
325 +      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
326 +      osw << "# std. dev.: " << wStdDev << "\n";
327 +      
328 +      // Normalize by number of frames and write it out:
329 +      for (int i = 0; i < W_histogram_.size(); ++i) {
330 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
331 +        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
332 +      }
333 +      
334 +      osw.close();
335 +    } else {
336 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
337 +              (getOutputFileName() + "w").c_str());
338 +      painCave.isFatal = 1;
339 +      simError();  
340 +    }
341 +  }
342   }

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