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root/group/trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 3018 by gezelter, Fri Sep 22 01:41:11 2006 UTC vs.
Revision 3021 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_ = 3.0;
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> q_lm;
120 <    std::map<int,ComplexType> QBar_lm;
121 <    RealType QSq_l;
122 <    RealType Q_l;
123 <    ComplexType W_l;
124 <    ComplexType W_l_hat;
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  
133 –    // Set the l for the spherical harmonic, it doesn't change
134 –    sphericalHarmonic.setL(lNumber_);
135 –
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 163 | Line 169 | namespace oopse {
169  
170          myIndex = sd->getGlobalIndex();
171          nBonds = 0;
172 <        for (int m = -lNumber_; m <= lNumber_; m++) {
173 <          q_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 191 | 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 <                  q_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                }  
213              }
214            }
215          }
216 <        RealType ql = 0.0;
217 <        for(int m=-lNumber_; m<=lNumber_; m++) {          
218 <          ql += norm(QBar_lm[m]);
219 <        }        
220 <        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
221 <        collectHistogram(sqrt(ql)/(RealType)nBonds);
222 <
216 >        
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 >        collectHistogram(q_l);
227 >        
228          Nbonds += nBonds;
229 <        for (int m=-lNumber_; m<=lNumber_; m++) {
230 <          QBar_lm[m] += q_lm[m];
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 >          }
233          }
234        }
235      }
236 <
236 >      
237      // Normalize Qbar2
238 <    for (int m = -lNumber_;m <= lNumber_; m++){
239 <      QBar_lm[m] /= Nbonds;
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      // Find second order invariant Q_l
245      
246 <    QSq_l = 0.0;
247 <    for (int m = -lNumber_; m <= lNumber_; m++){
248 <      QSq_l += norm(QBar_lm[m]);
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 <    std::cout << "qsl = " << QSq_l << "\n";
231 <    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
254 >
255      
256      // Find Third Order Invariant W_l
257      
258 <    W_l = 0.0;
259 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
260 <      // Zero work array
261 <      for (int ii = 0; ii < mSize_; ii++){
262 <        THRCOF[ii] = 0.0;
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        }
241 –      // Get Wigner coefficients
242 –      m1Pass = (double)m1;
282        
283 <      Wigner3jm(&l_, &l_, &l_,
245 <                &m1Pass, &m2Min, &m2Max,
246 <                THRCOF, &mSize_, &error);
247 <      
248 <      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
249 <        m2 = (int)floor(m2Min) + mmm;
250 <        m3 = -m1-m2;
251 <        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
252 <      }
283 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
284      }
285      
286 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
256 <    
257 <    writeOrderParameter(Q_l, real(W_l_hat));    
286 >    writeOrderParameter(Q, W_hat);    
287    }
288  
289 <  void BondOrderParameter::collectHistogram(RealType q_l) {
289 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
290  
291 <    if (q_l >= MinQ_ && q_l < MaxQ_) {
292 <      int qbin = (q_l - MinQ_) / deltaQ_;
293 <      Q_histogram_[qbin] += 1;
294 <      Qcount_++;
295 <      sumQ_ += q_l;
296 <      sumQ2_ += q_l * q_l;
297 <    } else {
298 <      sprintf( painCave.errMsg,
299 <               "q_l value outside reasonable range\n");
300 <      painCave.severity = OOPSE_ERROR;
301 <      painCave.isFatal = 1;
302 <      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  
305    }  
306  
307  
308 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
309 <
308 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
309 >    
310      std::ofstream os(getOutputFileName().c_str());
311 <
311 >    
312      if (os.is_open()) {
313        
314        os << "# Bond Order Parameters\n";
315        os << "# selection: (" << selectionScript_ << ")\n";
316 <      os << "# \n";
317 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
318 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\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 <        os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\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        }
330  
331        os.close();

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