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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 3005 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
Revision 3024 by gezelter, Tue Sep 26 14:33:56 2006 UTC

# Line 45 | Line 45
45   *     Phys Rev B, 28,784,1983
46   *
47   */
48 <
48 >
49   #include "applications/staticProps/BondOrderParameter.hpp"
50   #include "utils/simError.h"
51   #include "io/DumpReader.hpp"
52   #include "primitives/Molecule.hpp"
53   #include "utils/NumericConstant.hpp"
54 < #include "math/RealSphericalHarmonic.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 nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61 +    
62 +    setOutputName(getPrefix(filename) + ".bo");
63  
64 <  BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
65 <                                         const std::string& sele2, double rCut, int lNumber)
66 <    : StaticAnalyser(info, filename),
67 <      selectionScript1_(sele1), evaluator1_(info),
62 <      seleMan1_(info){
64 >    evaluator_.loadScriptString(sele);
65 >    if (!evaluator_.isDynamic()) {
66 >      seleMan_.setSelectionSet(evaluator_.evaluate());
67 >    }
68  
69 <    setOutputName(getPrefix(filename) + ".obo");
69 >    // Set up cutoff radius and order of the Legendre Polynomial:
70  
71 <    evaluator1_.loadScriptString(sele1);
72 <    evaluator2_.loadScriptString(sele2);
71 >    rCut_ = rCut;
72 >    nBins_ = nbins;
73 >    Qcount_.resize(lMax_+1);
74 >    Wcount_.resize(lMax_+1);
75  
76 <    if (!evaluator1_.isDynamic()) {
70 <      seleMan1_.setSelectionSet(evaluator1_.evaluate());
71 <    }else {
72 <      sprintf( painCave.errMsg,
73 <               "--sele1 must be static selection\n");
74 <      painCave.severity = OOPSE_ERROR;
75 <      painCave.isFatal = 1;
76 <      simError();
77 <    }
76 >    // Q can take values from 0 to 1
77  
78 <    /* Set up cutoff radius and type of order parameter we are calcuating*/
79 <    lNumber_ = lNumber;
80 <    rCut_ = rCut;
82 <    mSize_ = 2*lNumber_+1;
78 >    MinQ_ = 0.0;
79 >    MaxQ_ = 1.1;
80 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81  
82 <    int i;
83 <    int j;
86 <    StuntDouble* sd1;
87 <    StuntDouble* sd2;
88 <    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
89 <         sd1 != NULL && sd2 != NULL;
90 <         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
91 <      for (sd2 = seleMan1_.beginSelected(j),sd2
92 <             sdPairs_.push_back(std::make_pair(sd1, sd2));
93 <           }
82 >    // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
83 >    // use values for MinW_ and MaxW_ that are slightly larger than this:
84  
85 +    MinW_ = -0.25;
86 +    MaxW_ = 0.25;
87 +    deltaW_ = (MaxW_ - MinW_) / nbins;
88  
89 +    // Make arrays for Wigner3jm
90 +    double* THRCOF = new double[2*lMax_+1];
91 +    // Variables for Wigner routine
92 +    double lPass, m1Pass, m2m, m2M;
93 +    int error, mSize;
94 +    mSize = 2*lMax_+1;
95 +
96 +    for (int l = 0; l <= lMax_; l++) {
97 +      lPass = (double)l;
98 +      for (int m1 = -l; m1 <= l; m1++) {
99 +        m1Pass = (double)m1;
100 +
101 +        std::pair<int,int> lm = std::make_pair(l, m1);
102 +        
103 +        // Zero work array
104 +        for (int ii = 0; ii < 2*l + 1; ii++){
105 +          THRCOF[ii] = 0.0;
106 +        }
107 +            
108 +        // Get Wigner coefficients
109 +        Wigner3jm(&lPass, &lPass, &lPass,
110 +                  &m1Pass, &m2m, &m2M,
111 +                  THRCOF, &mSize, &error);
112 +        
113 +        m2Min[lm] = (int)floor(m2m);
114 +        m2Max[lm] = (int)floor(m2M);
115 +        
116 +        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
117 +          w3j[lm].push_back(THRCOF[mmm]);
118 +        }
119 +      }
120      }
121 +  }
122 +  
123 +  BondOrderParameter::~BondOrderParameter() {
124 +    Q_histogram_.clear();
125 +    W_histogram_.clear();
126 +  }
127  
128 <    void BondOrderParameter::process
129 <      () {
130 <      Molecule* mol;
131 <      RigidBody* rb;
132 <      SimInfo::MoleculeIterator mi;
133 <      Molecule::RigidBodyIterator rbIter;
134 <      RealType theta;
135 <      RealType phi;
106 <      RealType r;
107 <      RealType dist;
108 <      RealType* QBar_lm;
109 <      RealType QSq_l;
110 <      int nBonds;
111 <      int m, m_index;
112 <      RealSphericalHarmonic sphericalHarmonic;
128 >  void BondOrderParameter::initalizeHistogram() {
129 >    for (int bin = 0; bin < nBins_; bin++) {
130 >      for (int l = 0; l <= lMax_; l++) {
131 >        Q_histogram_[std::make_pair(bin,l)] = 0;
132 >        W_histogram_[std::make_pair(bin,l)] = 0;
133 >      }
134 >    }
135 >  }
136  
137 +  void BondOrderParameter::process() {
138 +    Molecule* mol;
139 +    Atom* atom;
140 +    RigidBody* rb;
141 +    int myIndex;
142 +    SimInfo::MoleculeIterator mi;
143 +    Molecule::RigidBodyIterator rbIter;
144 +    Molecule::AtomIterator ai;
145 +    StuntDouble* sd;
146 +    Vector3d vec;
147 +    RealType costheta;
148 +    RealType phi;
149 +    RealType r;
150 +    RealType dist;
151 +    std::map<std::pair<int,int>,ComplexType> q;
152 +    std::vector<RealType> q_l;
153 +    std::vector<RealType> q2;
154 +    std::vector<ComplexType> w;
155 +    std::vector<ComplexType> w_hat;
156 +    std::map<std::pair<int,int>,ComplexType> QBar;
157 +    std::vector<RealType> Q2;
158 +    std::vector<RealType> Q;
159 +    std::vector<ComplexType> W;
160 +    std::vector<ComplexType> W_hat;
161 +    int nBonds, Nbonds;
162 +    SphericalHarmonic sphericalHarmonic;
163 +    int i, j;
164  
165 <      DumpReader reader(info_, dumpFilename_);
166 <      int nFrames = reader.getNFrames();
165 >    DumpReader reader(info_, dumpFilename_);    
166 >    int nFrames = reader.getNFrames();
167 >    frameCounter_ = 0;
168  
169 <      /*Set the l for the spherical harmonic, it doesn't change*/
170 <      sphericalHarmonic.setL(lNumber_);
169 >    q_l.resize(lMax_+1);
170 >    q2.resize(lMax_+1);
171 >    w.resize(lMax_+1);
172 >    w_hat.resize(lMax_+1);
173  
174 <      for (int i = 0; i < nFrames; i += step_) {
175 <        reader.readFrame(i);
176 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
177 <        nBonds = 0;
174 >    Q2.resize(lMax_+1);
175 >    Q.resize(lMax_+1);
176 >    W.resize(lMax_+1);
177 >    W_hat.resize(lMax_+1);
178  
179 <        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
180 <          //change the positions of atoms which belong to the rigidbodies
181 <          for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
182 <            rb->updateAtoms();
183 <          }
179 >    for (int istep = 0; istep < nFrames; istep += step_) {
180 >      reader.readFrame(istep);
181 >      frameCounter_++;
182 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
183 >      
184 >      if (evaluator_.isDynamic()) {
185 >        seleMan_.setSelectionSet(evaluator_.evaluate());
186 >      }
187  
188 <        }
188 >      // update the positions of atoms which belong to the rigidbodies
189  
190 +      for (mol = info_->beginMolecule(mi); mol != NULL;
191 +           mol = info_->nextMolecule(mi)) {
192 +        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
193 +             rb = mol->nextRigidBody(rbIter)) {
194 +          rb->updateAtoms();
195 +        }        
196 +      }          
197 +            
198 +      // outer loop is over the selected StuntDoubles:
199  
200 <        /* Setup QBar */
201 <        QBar_lm = new double[mSize_];
200 >      for (sd = seleMan_.beginSelected(i); sd != NULL;
201 >           sd = seleMan_.nextSelected(i)) {
202  
203 <        /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
204 <        for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
205 <          Vector3d vec = j->first->getPos() - j->second->getPos();
206 <          currentSnapshot_->wrapVector(vec);
207 <          /* The spherical harmonics are wrt any arbitray coordiate sysetm,
208 <           * we choose standard spherical coordinates */
209 <          r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
203 >        myIndex = sd->getGlobalIndex();
204 >        nBonds = 0;
205 >        
206 >        for (int l = 0; l <= lMax_; l++) {
207 >          for (int m = -l; m <= l; m++) {
208 >            q[std::make_pair(l,m)] = 0.0;
209 >          }
210 >        }
211 >        
212 >        // inner loop is over all other atoms in the system:
213 >        
214 >        for (mol = info_->beginMolecule(mi); mol != NULL;
215 >             mol = info_->nextMolecule(mi)) {
216 >          for (atom = mol->beginAtom(ai); atom != NULL;
217 >               atom = mol->nextAtom(ai)) {
218  
219 <          /* Check to see if neighbor is in bond cuttoff*/
147 <          if (r<rCut_){
148 <            theta = atan(vec.y()/vec.x());
149 <            phi = acos(vec.z()/r);
150 <            for(int m_index = 0; m_index < mSize_; m_index++){
151 <              sphericalHarmonic.setM(m_index-lNumber_);
152 <              QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
153 <            }
154 <            nBonds++;
155 <          }
156 <        }
219 >            if (atom->getGlobalIndex() != myIndex) {
220  
221 <        /*Normalize Qbar by number of Bonds*/
222 <        for ( int m_index = 0;m_index < mSize_; m_index++){
223 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
224 <        }
221 >              vec = sd->getPos() - atom->getPos();      
222 >              currentSnapshot_->wrapVector(vec);
223 >              
224 >              // Calculate "bonds" and build Q_lm(r) where
225 >              //      Q_lm = Y_lm(theta(r),phi(r))                
226 >              // The spherical harmonics are wrt any arbitrary coordinate
227 >              // system, we choose standard spherical coordinates
228 >              
229 >              r = vec.length();
230 >              
231 >              // Check to see if neighbor is in bond cutoff
232 >              
233 >              if (r < rCut_) {
234 >                costheta = vec.z() / r;
235 >                phi = atan2(vec.y(), vec.x());
236  
237 +                for (int l = 0; l <= lMax_; l++) {
238 +                  sphericalHarmonic.setL(l);
239 +                  for(int m = -l; m <= l; m++){
240 +                    sphericalHarmonic.setM(m);
241 +                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
242 +                  }
243 +                }
244 +                nBonds++;
245 +              }  
246 +            }
247 +          }
248 +        }
249 +        
250 +        
251 +        for (int l = 0; l <= lMax_; l++) {        
252 +          q_l[l] = 0.0;
253 +          for(int m = -l; m <= l; m++) {
254 +            q_l[l] += norm(q[std::make_pair(l,m)]);
255 +          }    
256 +          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
257 +          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
258 +        }
259  
260 <      }
260 >        // Find second order invariant Q_l
261 >        
262 >        for (int l = 0; l <= lMax_; l++) {
263 >          q2[l] = 0.0;
264 >          for (int m = -l; m <= l; m++){
265 >            q2[l] += norm(q[std::make_pair(l,m)]);
266 >          }
267 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
268 >                        (RealType)(2*l + 1))/(RealType)nBonds;
269 >        }
270  
271 <      /*Normalize by number of frames*/
272 <      for ( int m_index = 0;m_index < mSize_; m_index++){
273 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
271 >        // Find Third Order Invariant W_l
272 >    
273 >        for (int l = 0; l <= lMax_; l++) {
274 >          w[l] = 0.0;
275 >          for (int m1 = -l; m1 <= l; m1++) {
276 >            std::pair<int,int> lm = std::make_pair(l, m1);
277 >            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
278 >              int m2 = m2Min[lm] + mmm;
279 >              int m3 = -m1-m2;
280 >              w[l] += w3j[lm][mmm] * q[lm] *
281 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
282 >            }
283 >          }
284 >          
285 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
286 >        }
287 >
288 >        collectHistogram(q_l, w_hat);
289 >        
290 >        Nbonds += nBonds;
291 >        for (int l = 0; l <= lMax_;  l++) {
292 >          for (int m = -l; m <= l; m++) {
293 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
294 >          }
295 >        }
296        }
297 +    }
298 +      
299 +    // Normalize Qbar2
300 +    for (int l = 0; l <= lMax_; l++) {
301 +      for (int m = -l; m <= l; m++){
302 +        QBar[std::make_pair(l,m)] /= Nbonds;
303 +      }
304 +    }
305 +    
306 +    // Find second order invariant Q_l
307 +    
308 +    for (int l = 0; l <= lMax_; l++) {
309 +      Q2[l] = 0.0;
310 +      for (int m = -l; m <= l; m++){
311 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
312 +      }
313 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
314 +    }
315 +    
316 +    // Find Third Order Invariant W_l
317 +    
318 +    for (int l = 0; l <= lMax_; l++) {
319 +      W[l] = 0.0;
320 +      for (int m1 = -l; m1 <= l; m1++) {
321 +        std::pair<int,int> lm = std::make_pair(l, m1);
322 +        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
323 +          int m2 = m2Min[lm] + mmm;
324 +          int m3 = -m1-m2;
325 +          W[l] += w3j[lm][mmm] * QBar[lm] *
326 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
327 +        }
328 +      }
329 +      
330 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
331 +    }
332 +    
333 +    writeOrderParameter(Q, W_hat);    
334 +  }
335  
336 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 +                                            std::vector<ComplexType> what) {
338  
339 +    for (int l = 0; l <= lMax_; l++) {
340 +      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
341 +        int qbin = (q[l] - MinQ_) / deltaQ_;
342 +        Q_histogram_[std::make_pair(qbin,l)] += 1;
343 +        Qcount_[l]++;      
344 +      } else {
345 +        sprintf( painCave.errMsg,
346 +                 "q_l value outside reasonable range\n");
347 +        painCave.severity = OOPSE_ERROR;
348 +        painCave.isFatal = 1;
349 +        simError();  
350 +      }
351 +    }
352  
353 <      /* Find second order invariant Q_l*/
354 <
355 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
356 <        QSq_l += pow(QBar_lm(m),2);
353 >    for (int l = 0; l <= lMax_; l++) {
354 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
355 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
356 >        W_histogram_[std::make_pair(wbin,l)] += 1;
357 >        Wcount_[l]++;      
358 >      } else {
359 >        sprintf( painCave.errMsg,
360 >                 "Re[w_hat] value outside reasonable range\n");
361 >        painCave.severity = OOPSE_ERROR;
362 >        painCave.isFatal = 1;
363 >        simError();  
364        }
365 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
365 >    }
366  
367 <      /* Find Third Order Invariant W_l*/
367 >  }  
368  
182 –      /* Make arrays for Wigner3jm */
183 –      double* THRCOF = new double[mSize_];
184 –      /* Variables for Wigner routine */
185 –      double l_ = (double)lNumber_;
186 –      double m2Min;
187 –      double m2Max;
188 –      int error;
189 –      int m1;
190 –      int m2;
191 –      int m3;
369  
370 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
371 <        /* Zero work array */
372 <        for (i=0; i<mSize_;i++){
373 <          THRCOF[i] = 0.0;      
374 <        }
375 <        /* Get wigner coefficients */
376 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
377 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
378 <          m2 = floor(m2Min) + m_index - 1;
379 <          m3 = -m1-m2;
380 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
381 <        }
370 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 >                                               std::vector<ComplexType> What) {
372 >    
373 >    std::ofstream osq((getOutputFileName() + "q").c_str());
374 >
375 >    if (osq.is_open()) {
376 >      
377 >      osq << "# Bond Order Parameters\n";
378 >      osq << "# selection: (" << selectionScript_ << ")\n";
379 >      osq << "# \n";
380 >      for (int l = 0; l <= lMax_; l++) {
381 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
382        }
383 +      // Normalize by number of frames and write it out:
384 +      for (int i = 0; i < nBins_; ++i) {
385 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
386 +        osq << Qval;
387 +        for (int l = 0; l <= lMax_; l++) {
388 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
389 +        }
390 +        osq << "\n";
391 +      }
392  
393 +      osq.close();
394  
395 <      writeOrderParameter();
396 <
395 >    } else {
396 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
397 >              (getOutputFileName() + "q").c_str());
398 >      painCave.isFatal = 1;
399 >      simError();  
400      }
401  
402 +    std::ofstream osw((getOutputFileName() + "w").c_str());
403  
404 <    void BondOrderParameter::writeOrderParameter() {
405 <
406 <      std::ofstream os(getOutputFileName().c_str());
407 <      os << "#radial distribution function\n";
408 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
409 <      os << "selection2: (" << selectionScript2_ << ")\n";
219 <      os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
220 <
221 <      for (std::size_t i = 0; i < orderParams_.size(); ++i) {
222 <        os <<  orderParams_[i].p2 << "\t"
223 <           <<  orderParams_[i].director[0] << "\t"
224 <           <<  orderParams_[i].director[1] << "\t"
225 <           <<  orderParams_[i].director[2] << "\t"
226 <           <<  orderParams_[i].angle << "\n";
227 <
404 >    if (osw.is_open()) {
405 >      osw << "# Bond Order Parameters\n";
406 >      osw << "# selection: (" << selectionScript_ << ")\n";
407 >      osw << "# \n";
408 >      for (int l = 0; l <= lMax_; l++) {
409 >        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
410        }
411 +      // Normalize by number of frames and write it out:
412 +      for (int i = 0; i < nBins_; ++i) {
413 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
414 +        osw << Wval;
415 +        for (int l = 0; l <= lMax_; l++) {
416 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
417 +        }
418 +        osw << "\n";
419 +      }
420  
421 +      osw.close();
422 +    } else {
423 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
424 +              (getOutputFileName() + "w").c_str());
425 +      painCave.isFatal = 1;
426 +      simError();  
427      }
428 <
428 >      
429    }
430 <
430 > }

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