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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 1043 by gezelter, Thu Sep 21 14:45:08 2006 UTC vs.
Revision 1051 by gezelter, Mon Sep 25 22:08:33 2006 UTC

# Line 51 | Line 51
51   #include "io/DumpReader.hpp"
52   #include "primitives/Molecule.hpp"
53   #include "utils/NumericConstant.hpp"
54 – #include "math/SphericalHarmonic.hpp"
54  
55   namespace oopse {
56  
57    BondOrderParameter::BondOrderParameter(SimInfo* info,
58                                           const std::string& filename,
59                                           const std::string& sele,
60 <                                         double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
60 >                                         double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61      
62      setOutputName(getPrefix(filename) + ".bo");
63  
# Line 69 | Line 68 | namespace oopse {
68  
69      // Set up cutoff radius and order of the Legendre Polynomial:
70  
71 <    lNumber_ = lNumber;
71 >    lMax_ = lMax;
72      rCut_ = rCut;
73 <    mSize_ = 2*lNumber_+1;    
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_ = 1.0;
80 >    MaxQ_ = 1.1;
81      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:
# Line 86 | Line 86 | namespace oopse {
86      MinW_ = -0.18;
87      MaxW_ = 0.18;
88      deltaW_ = (MaxW_ - MinW_) / nbins;
89 –    W_histogram_.resize(nbins);
90 –
89    }
90  
91    BondOrderParameter::~BondOrderParameter() {
# Line 96 | Line 94 | namespace oopse {
94    }
95  
96    void BondOrderParameter::initalizeHistogram() {
97 <    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
98 <    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
97 >    for (int bin = 0; bin < nBins_; bin++) {
98 >      for (int l = 0; l <= lMax_; l++) {
99 >        Q_histogram_[std::make_pair(bin,l)] = 0;
100 >        W_histogram_[std::make_pair(bin,l)] = 0;
101 >      }
102 >    }
103    }
104  
105    void BondOrderParameter::process() {
# Line 114 | Line 116 | namespace oopse {
116      RealType phi;
117      RealType r;
118      RealType dist;
119 <    std::map<int, ComplexType> QBar_lm;
120 <    RealType QSq_l;
121 <    RealType Q_l;
122 <    ComplexType W_l;
123 <    ComplexType W_l_hat;
124 <    int nBonds;
119 >    std::map<std::pair<int,int>,ComplexType> q;
120 >    std::vector<RealType> q_l;
121 >    std::map<std::pair<int,int>,ComplexType> QBar;
122 >    std::vector<RealType> Q2;
123 >    std::vector<RealType> Q;
124 >    std::vector<ComplexType> W;
125 >    std::vector<ComplexType> W_hat;
126 >    int nBonds, Nbonds;
127      SphericalHarmonic sphericalHarmonic;
128      int i, j;
129      // Make arrays for Wigner3jm
130 <    double* THRCOF = new double[mSize_];
130 >    double* THRCOF = new double[2*lMax_+1];
131      // Variables for Wigner routine
132 <    double l_ = (double)lNumber_;
133 <    double m1Pass, m2Min, m2Max;
134 <    int error, m1, m2, m3;
132 >    double lPass, m1Pass, m2Min, m2Max;
133 >    int error, m1, m2, m3, mSize;
134 >    mSize = 2*lMax_+1;
135  
132 –    // Set the l for the spherical harmonic, it doesn't change
133 –    sphericalHarmonic.setL(lNumber_);
134 –
136      DumpReader reader(info_, dumpFilename_);    
137      int nFrames = reader.getNFrames();
138      frameCounter_ = 0;
139  
140 +    q_l.resize(lMax_+1);
141 +    Q2.resize(lMax_+1);
142 +    Q.resize(lMax_+1);
143 +    W.resize(lMax_+1);
144 +    W_hat.resize(lMax_+1);
145 +
146      for (int istep = 0; istep < nFrames; istep += step_) {
147        reader.readFrame(istep);
148        frameCounter_++;
# Line 153 | Line 160 | namespace oopse {
160               rb = mol->nextRigidBody(rbIter)) {
161            rb->updateAtoms();
162          }        
163 <      }      
164 <      
163 >      }          
164 >            
165        // outer loop is over the selected StuntDoubles:
166  
167        for (sd = seleMan_.beginSelected(i); sd != NULL;
168             sd = seleMan_.nextSelected(i)) {
169  
170          myIndex = sd->getGlobalIndex();
164 –
165 –        // For this central atom, zero out nBonds and QBar_lm
166 –
171          nBonds = 0;
172 <      
173 <        for (int m = -lNumber_; m <= lNumber_; m++) {
174 <          QBar_lm[m] = 0.0;
172 >        
173 >        for (int l = 0; l <= lMax_; l++) {
174 >          for (int m = -l; m <= l; m++) {
175 >            q[std::make_pair(l,m)] = 0.0;
176 >          }
177          }
178          
179          // inner loop is over all other atoms in the system:
# Line 194 | Line 200 | namespace oopse {
200                if (r < rCut_) {
201                  costheta = vec.z() / r;
202                  phi = atan2(vec.y(), vec.x());
203 <                
204 <                for(int m = -lNumber_; m <= lNumber_; m++){
205 <                  sphericalHarmonic.setM(m);
206 <                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
203 >
204 >                for (int l = 0; l <= lMax_; l++) {
205 >                  sphericalHarmonic.setL(l);
206 >                  for(int m = -l; m <= l; m++){
207 >                    sphericalHarmonic.setM(m);
208 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
209 >                  }
210                  }
211                  nBonds++;
212                }  
# Line 205 | Line 214 | namespace oopse {
214            }
215          }
216          
217 <        // Normalize Qbar2
218 <        for (int m = -lNumber_;m <= lNumber_; m++){
219 <          QBar_lm[m] /= nBonds;
220 <          std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
217 >        
218 >        for (int l = 0; l <= lMax_; l++) {        
219 >          q_l[l] = 0.0;
220 >          for(int m = -l; m <= l; m++) {
221 >            q_l[l] += norm(q[std::make_pair(l,m)]);
222 >          }    
223 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
224 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
225          }
226 <
214 <        // Find second order invariant Q_l
215 <
216 <        QSq_l = 0.0;
217 <        for (int m = -lNumber_; m <= lNumber_; m++){
218 <          QSq_l += norm(QBar_lm[m]);
219 <        }
220 <        std::cout << "qsq_l = " << QSq_l << "\n";
221 <        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
222 <
223 <        // Find Third Order Invariant W_l
226 >        collectHistogram(q_l);
227          
228 <        W_l = 0.0;
229 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
230 <          // Zero work array
231 <          for (int ii = 0; ii < mSize_; ii++){
229 <            THRCOF[i] = 0.0;
228 >        Nbonds += nBonds;
229 >        for (int l = 0; l <= lMax_;  l++) {
230 >          for (int m = -l; m <= l; m++) {
231 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
232            }
231 –          // Get Wigner coefficients
232 –          m1Pass = (double)m1;
233 –          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
234 –          for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
235 –            m2 = floor(m2Min) + m_index - 1;
236 –            m3 = -m1-m2;
237 –            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
238 –          }
233          }
240 –        
241 –        W_l_hat = W_l / pow(QSq_l, 1.5);
242 –        
243 –        // accumulate histogram data for Q_l and W_l_hat:
244 –
245 –        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
246 –        collectHistogram(Q_l, real(W_l_hat));
247 –                
234        }
235      }
236 +      
237 +    // Normalize Qbar2
238 +    for (int l = 0; l <= lMax_; l++) {
239 +      for (int m = -l; m <= l; m++){
240 +        QBar[std::make_pair(l,m)] /= Nbonds;
241 +      }
242 +    }
243      
244 <    writeOrderParameter();
244 >    // Find second order invariant Q_l
245      
246 +    for (int l = 0; l <= lMax_; l++) {
247 +      Q2[l] = 0.0;
248 +      for (int m = -l; m <= l; m++){
249 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
250 +      }
251 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
252 +    }
253 +    
254 +
255 +    
256 +    // Find Third Order Invariant W_l
257 +    
258 +    for (int l = 0; l <= lMax_; l++) {
259 +      W[l] = 0.0;
260 +      lPass = (double)l;
261 +      for (int m1 = -l; m1 <= l; m1++) {
262 +        // Zero work array
263 +        for (int ii = 0; ii < 2*l + 1; ii++){
264 +          THRCOF[ii] = 0.0;
265 +        }
266 +        // Get Wigner coefficients
267 +        m1Pass = (double)m1;
268 +        
269 +        Wigner3jm(&lPass, &lPass, &lPass,
270 +                  &m1Pass, &m2Min, &m2Max,
271 +                  THRCOF, &mSize, &error);
272 +        
273 +        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
274 +          m2 = (int)floor(m2Min) + mmm;
275 +          m3 = -m1-m2;
276 +          W[l] += THRCOF[mmm] *
277 +            QBar[std::make_pair(l,m1)] *
278 +            QBar[std::make_pair(l,m2)] *
279 +            QBar[std::make_pair(l,m3)];
280 +        }
281 +      }
282 +      
283 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
284 +    }
285 +    
286 +    writeOrderParameter(Q, W_hat);    
287    }
288  
289 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
290  
291 <  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
292 <
293 <    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
294 <      int qbin = (Q_l - MinQ_) / deltaQ_;
295 <      Q_histogram_[qbin] += 1;
296 <      Qcount_++;
297 <      sumQ_ += Q_l;
298 <      sumQ2_ += Q_l * Q_l;
299 <    } else {
300 <      sprintf( painCave.errMsg,
301 <               "Q_l value outside reasonable range\n");
302 <      painCave.severity = OOPSE_ERROR;
268 <      painCave.isFatal = 1;
269 <      simError();  
291 >    for (int l = 0; l <= lMax_; l++) {
292 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
293 >        int qbin = (q[l] - MinQ_) / deltaQ_;
294 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
295 >        Qcount_[l]++;      
296 >      } else {
297 >        sprintf( painCave.errMsg,
298 >                 "q_l value outside reasonable range\n");
299 >        painCave.severity = OOPSE_ERROR;
300 >        painCave.isFatal = 1;
301 >        simError();  
302 >      }
303      }
304  
272 –    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
273 –      int wbin = (W_l_hat - MinW_) / deltaW_;
274 –      W_histogram_[wbin] += 1;
275 –      Wcount_++;
276 –      sumW_  += W_l_hat;
277 –      sumW2_ += W_l_hat*W_l_hat;
278 –    } else {
279 –      sprintf( painCave.errMsg,
280 –               "W_l_hat value outside reasonable range\n");
281 –      painCave.severity = OOPSE_ERROR;
282 –      painCave.isFatal = 1;
283 –      simError();  
284 –    }
305    }  
306  
287 –  void BondOrderParameter::writeOrderParameter() {
307  
308 <    std::ofstream osq((getOutputFileName() + "q").c_str());
309 <
310 <    if (osq.is_open()) {
311 <
312 <      RealType qAvg = sumQ_ / (RealType) Qcount_;
294 <      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
308 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
309 >    
310 >    std::ofstream os(getOutputFileName().c_str());
311 >    
312 >    if (os.is_open()) {
313        
314 <      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
315 <      osq << "# selection: (" << selectionScript_ << ")\n";
316 <      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
317 <      osq << "# std. dev.: " << qStdDev << "\n";
318 <      
314 >      os << "# Bond Order Parameters\n";
315 >      os << "# selection: (" << selectionScript_ << ")\n";
316 >      for (int l = 0; l <= lMax_; l++) {
317 >        os << "# \n";
318 >        os << "# <Q_" << l << ">: " << Q[l] << "\n";
319 >        os << "# <W_" << l << ">: " << real(What[l]) << "\n";
320 >      }
321        // Normalize by number of frames and write it out:
322 <      for (int i = 0; i < Q_histogram_.size(); ++i) {
323 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
324 <        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
322 >      for (int i = 0; i < nBins_; ++i) {
323 >        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
324 >        os << Qval;
325 >        for (int l = 0; l <= lMax_; l++) {
326 >          os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
327 >        }
328 >        os << "\n";
329        }
306 –      
307 –      osq.close();
308 –    } else {
309 –      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
310 –              (getOutputFileName() + "q").c_str());
311 –      painCave.isFatal = 1;
312 –      simError();  
313 –    }
330  
331 <    std::ofstream osw((getOutputFileName() + "w").c_str());
331 >      os.close();
332  
317 –    if (osw.is_open()) {
318 –
319 –      RealType wAvg = sumW_ / (RealType) Wcount_;
320 –      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
321 –      
322 –      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
323 –      osw << "# selection: (" << selectionScript_ << ")\n";
324 –      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
325 –      osw << "# std. dev.: " << wStdDev << "\n";
326 –      
327 –      // Normalize by number of frames and write it out:
328 –      for (int i = 0; i < W_histogram_.size(); ++i) {
329 –        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
330 –        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
331 –      }
332 –      
333 –      osw.close();
333      } else {
334        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
335 <              (getOutputFileName() + "w").c_str());
335 >              getOutputFileName().c_str());
336        painCave.isFatal = 1;
337        simError();  
338      }

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