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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 3022 by gezelter, Tue Sep 26 01:30:32 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  
90 +  BondOrderParameter::~BondOrderParameter() {
91 +    Q_histogram_.clear();
92 +    W_histogram_.clear();
93 +  }
94 +
95 +  void BondOrderParameter::initalizeHistogram() {
96 +    for (int bin = 0; bin < nBins_; bin++) {
97 +      for (int l = 0; l <= lMax_; l++) {
98 +        Q_histogram_[std::make_pair(bin,l)] = 0;
99 +        W_histogram_[std::make_pair(bin,l)] = 0;
100 +      }
101      }
102 +  }
103  
104 <    void BondOrderParameter::process
105 <      () {
106 <      Molecule* mol;
107 <      RigidBody* rb;
108 <      SimInfo::MoleculeIterator mi;
109 <      Molecule::RigidBodyIterator rbIter;
110 <      RealType theta;
111 <      RealType phi;
112 <      RealType r;
113 <      RealType dist;
114 <      RealType* QBar_lm;
115 <      RealType QSq_l;
116 <      int nBonds;
117 <      int m, m_index;
118 <      RealSphericalHarmonic sphericalHarmonic;
104 >  void BondOrderParameter::process() {
105 >    Molecule* mol;
106 >    Atom* atom;
107 >    RigidBody* rb;
108 >    int myIndex;
109 >    SimInfo::MoleculeIterator mi;
110 >    Molecule::RigidBodyIterator rbIter;
111 >    Molecule::AtomIterator ai;
112 >    StuntDouble* sd;
113 >    Vector3d vec;
114 >    RealType costheta;
115 >    RealType phi;
116 >    RealType r;
117 >    RealType dist;
118 >    std::map<std::pair<int,int>,ComplexType> q;
119 >    std::vector<RealType> q_l;
120 >    std::vector<RealType> q2;
121 >    std::vector<ComplexType> w;
122 >    std::vector<ComplexType> w_hat;
123 >    std::map<std::pair<int,int>,ComplexType> QBar;
124 >    std::vector<RealType> Q2;
125 >    std::vector<RealType> Q;
126 >    std::vector<ComplexType> W;
127 >    std::vector<ComplexType> W_hat;
128 >    int nBonds, Nbonds;
129 >    SphericalHarmonic sphericalHarmonic;
130 >    int i, j;
131 >    // Make arrays for Wigner3jm
132 >    double* THRCOF = new double[2*lMax_+1];
133 >    // Variables for Wigner routine
134 >    double lPass, m1Pass, m2Min, m2Max;
135 >    int error, m1, m2, m3, mSize;
136 >    mSize = 2*lMax_+1;
137  
138 +    DumpReader reader(info_, dumpFilename_);    
139 +    int nFrames = reader.getNFrames();
140 +    frameCounter_ = 0;
141  
142 <      DumpReader reader(info_, dumpFilename_);
143 <      int nFrames = reader.getNFrames();
142 >    q_l.resize(lMax_+1);
143 >    q2.resize(lMax_+1);
144 >    w.resize(lMax_+1);
145 >    w_hat.resize(lMax_+1);
146  
147 <      /*Set the l for the spherical harmonic, it doesn't change*/
148 <      sphericalHarmonic.setL(lNumber_);
147 >    Q2.resize(lMax_+1);
148 >    Q.resize(lMax_+1);
149 >    W.resize(lMax_+1);
150 >    W_hat.resize(lMax_+1);
151  
152 <      for (int i = 0; i < nFrames; i += step_) {
153 <        reader.readFrame(i);
154 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
155 <        nBonds = 0;
152 >    for (int istep = 0; istep < nFrames; istep += step_) {
153 >      reader.readFrame(istep);
154 >      frameCounter_++;
155 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
156 >      
157 >      if (evaluator_.isDynamic()) {
158 >        seleMan_.setSelectionSet(evaluator_.evaluate());
159 >      }
160  
161 <        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
127 <          //change the positions of atoms which belong to the rigidbodies
128 <          for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
129 <            rb->updateAtoms();
130 <          }
161 >      // update the positions of atoms which belong to the rigidbodies
162  
163 <        }
163 >      for (mol = info_->beginMolecule(mi); mol != NULL;
164 >           mol = info_->nextMolecule(mi)) {
165 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
166 >             rb = mol->nextRigidBody(rbIter)) {
167 >          rb->updateAtoms();
168 >        }        
169 >      }          
170 >            
171 >      // outer loop is over the selected StuntDoubles:
172  
173 +      for (sd = seleMan_.beginSelected(i); sd != NULL;
174 +           sd = seleMan_.nextSelected(i)) {
175  
176 <        /* Setup QBar */
177 <        QBar_lm = new double[mSize_];
176 >        myIndex = sd->getGlobalIndex();
177 >        nBonds = 0;
178 >        
179 >        for (int l = 0; l <= lMax_; l++) {
180 >          for (int m = -l; m <= l; m++) {
181 >            q[std::make_pair(l,m)] = 0.0;
182 >          }
183 >        }
184 >        
185 >        // inner loop is over all other atoms in the system:
186 >        
187 >        for (mol = info_->beginMolecule(mi); mol != NULL;
188 >             mol = info_->nextMolecule(mi)) {
189 >          for (atom = mol->beginAtom(ai); atom != NULL;
190 >               atom = mol->nextAtom(ai)) {
191  
192 <        /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
139 <        for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
140 <          Vector3d vec = j->first->getPos() - j->second->getPos();
141 <          currentSnapshot_->wrapVector(vec);
142 <          /* The spherical harmonics are wrt any arbitray coordiate sysetm,
143 <           * we choose standard spherical coordinates */
144 <          r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
192 >            if (atom->getGlobalIndex() != myIndex) {
193  
194 <          /* Check to see if neighbor is in bond cuttoff*/
195 <          if (r<rCut_){
196 <            theta = atan(vec.y()/vec.x());
197 <            phi = acos(vec.z()/r);
198 <            for(int m_index = 0; m_index < mSize_; m_index++){
199 <              sphericalHarmonic.setM(m_index-lNumber_);
200 <              QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
201 <            }
202 <            nBonds++;
203 <          }
204 <        }
194 >              vec = sd->getPos() - atom->getPos();      
195 >              currentSnapshot_->wrapVector(vec);
196 >              
197 >              // Calculate "bonds" and build Q_lm(r) where
198 >              //      Q_lm = Y_lm(theta(r),phi(r))                
199 >              // The spherical harmonics are wrt any arbitrary coordinate
200 >              // system, we choose standard spherical coordinates
201 >              
202 >              r = vec.length();
203 >              
204 >              // Check to see if neighbor is in bond cutoff
205 >              
206 >              if (r < rCut_) {
207 >                costheta = vec.z() / r;
208 >                phi = atan2(vec.y(), vec.x());
209  
210 <        /*Normalize Qbar by number of Bonds*/
211 <        for ( int m_index = 0;m_index < mSize_; m_index++){
212 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
213 <        }
210 >                for (int l = 0; l <= lMax_; l++) {
211 >                  sphericalHarmonic.setL(l);
212 >                  for(int m = -l; m <= l; m++){
213 >                    sphericalHarmonic.setM(m);
214 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
215 >                  }
216 >                }
217 >                nBonds++;
218 >              }  
219 >            }
220 >          }
221 >        }
222 >        
223 >        
224 >        for (int l = 0; l <= lMax_; l++) {        
225 >          q_l[l] = 0.0;
226 >          for(int m = -l; m <= l; m++) {
227 >            q_l[l] += norm(q[std::make_pair(l,m)]);
228 >          }    
229 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
230 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231 >        }
232  
233 +        // Find second order invariant Q_l
234 +        
235 +        for (int l = 0; l <= lMax_; l++) {
236 +          q2[l] = 0.0;
237 +          for (int m = -l; m <= l; m++){
238 +            q2[l] += norm(q[std::make_pair(l,m)]);
239 +          }
240 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241 +                        (RealType)(2*l + 1))/(RealType)nBonds;
242 +        }
243  
244 <      }
244 >        // Find Third Order Invariant W_l
245 >    
246 >        for (int l = 0; l <= lMax_; l++) {
247 >          w[l] = 0.0;
248 >          lPass = (double)l;
249 >          for (int m1 = -l; m1 <= l; m1++) {
250 >            // Zero work array
251 >            for (int ii = 0; ii < 2*l + 1; ii++){
252 >              THRCOF[ii] = 0.0;
253 >            }
254 >            // Get Wigner coefficients
255 >            m1Pass = (double)m1;
256 >            
257 >            Wigner3jm(&lPass, &lPass, &lPass,
258 >                      &m1Pass, &m2Min, &m2Max,
259 >                      THRCOF, &mSize, &error);
260 >            
261 >            for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
262 >              m2 = (int)floor(m2Min) + mmm;
263 >              m3 = -m1-m2;
264 >              w[l] += THRCOF[mmm] *
265 >                q[std::make_pair(l,m1)] *
266 >                q[std::make_pair(l,m2)] *
267 >                q[std::make_pair(l,m3)];
268 >            }
269 >          }
270 >          
271 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
272 >        }
273  
274 <      /*Normalize by number of frames*/
275 <      for ( int m_index = 0;m_index < mSize_; m_index++){
276 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
274 >        collectHistogram(q_l, w_hat);
275 >        
276 >        Nbonds += nBonds;
277 >        for (int l = 0; l <= lMax_;  l++) {
278 >          for (int m = -l; m <= l; m++) {
279 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
280 >          }
281 >        }
282        }
283 +    }
284 +      
285 +    // Normalize Qbar2
286 +    for (int l = 0; l <= lMax_; l++) {
287 +      for (int m = -l; m <= l; m++){
288 +        QBar[std::make_pair(l,m)] /= Nbonds;
289 +      }
290 +    }
291 +    
292 +    // Find second order invariant Q_l
293 +    
294 +    for (int l = 0; l <= lMax_; l++) {
295 +      Q2[l] = 0.0;
296 +      for (int m = -l; m <= l; m++){
297 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
298 +      }
299 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
300 +    }
301 +    
302 +    // Find Third Order Invariant W_l
303 +    
304 +    for (int l = 0; l <= lMax_; l++) {
305 +      W[l] = 0.0;
306 +      lPass = (double)l;
307 +      for (int m1 = -l; m1 <= l; m1++) {
308 +        // Zero work array
309 +        for (int ii = 0; ii < 2*l + 1; ii++){
310 +          THRCOF[ii] = 0.0;
311 +        }
312 +        // Get Wigner coefficients
313 +        m1Pass = (double)m1;
314 +        
315 +        Wigner3jm(&lPass, &lPass, &lPass,
316 +                  &m1Pass, &m2Min, &m2Max,
317 +                  THRCOF, &mSize, &error);
318 +        
319 +        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
320 +          m2 = (int)floor(m2Min) + mmm;
321 +          m3 = -m1-m2;
322 +          W[l] += THRCOF[mmm] *
323 +            QBar[std::make_pair(l,m1)] *
324 +            QBar[std::make_pair(l,m2)] *
325 +            QBar[std::make_pair(l,m3)];
326 +        }
327 +      }
328 +      
329 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
330 +    }
331 +    
332 +    writeOrderParameter(Q, W_hat);    
333 +  }
334  
335 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336 +                                            std::vector<ComplexType> what) {
337  
338 +    for (int l = 0; l <= lMax_; l++) {
339 +      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
340 +        int qbin = (q[l] - MinQ_) / deltaQ_;
341 +        Q_histogram_[std::make_pair(qbin,l)] += 1;
342 +        Qcount_[l]++;      
343 +      } else {
344 +        sprintf( painCave.errMsg,
345 +                 "q_l value outside reasonable range\n");
346 +        painCave.severity = OOPSE_ERROR;
347 +        painCave.isFatal = 1;
348 +        simError();  
349 +      }
350 +    }
351  
352 <      /* Find second order invariant Q_l*/
353 <
354 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
355 <        QSq_l += pow(QBar_lm(m),2);
352 >    for (int l = 0; l <= lMax_; l++) {
353 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
354 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
355 >        W_histogram_[std::make_pair(wbin,l)] += 1;
356 >        Wcount_[l]++;      
357 >      } else {
358 >        sprintf( painCave.errMsg,
359 >                 "Re[w_hat] value outside reasonable range\n");
360 >        painCave.severity = OOPSE_ERROR;
361 >        painCave.isFatal = 1;
362 >        simError();  
363        }
364 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
364 >    }
365  
366 <      /* Find Third Order Invariant W_l*/
366 >  }  
367  
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;
368  
369 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
370 <        /* Zero work array */
371 <        for (i=0; i<mSize_;i++){
372 <          THRCOF[i] = 0.0;      
373 <        }
374 <        /* Get wigner coefficients */
375 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
376 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
377 <          m2 = floor(m2Min) + m_index - 1;
378 <          m3 = -m1-m2;
379 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
380 <        }
369 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370 >                                               std::vector<ComplexType> What) {
371 >    
372 >    std::ofstream osq((getOutputFileName() + "q").c_str());
373 >
374 >    if (osq.is_open()) {
375 >      
376 >      osq << "# Bond Order Parameters\n";
377 >      osq << "# selection: (" << selectionScript_ << ")\n";
378 >      osq << "# \n";
379 >      for (int l = 0; l <= lMax_; l++) {
380 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
381        }
382 +      // Normalize by number of frames and write it out:
383 +      for (int i = 0; i < nBins_; ++i) {
384 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
385 +        osq << Qval;
386 +        for (int l = 0; l <= lMax_; l++) {
387 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
388 +        }
389 +        osq << "\n";
390 +      }
391  
392 +      osq.close();
393  
394 <      writeOrderParameter();
395 <
394 >    } else {
395 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396 >              (getOutputFileName() + "q").c_str());
397 >      painCave.isFatal = 1;
398 >      simError();  
399      }
400  
401 +    std::ofstream osw((getOutputFileName() + "w").c_str());
402  
403 <    void BondOrderParameter::writeOrderParameter() {
404 <
405 <      std::ofstream os(getOutputFileName().c_str());
406 <      os << "#radial distribution function\n";
407 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
408 <      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 <
403 >    if (osw.is_open()) {
404 >      osw << "# Bond Order Parameters\n";
405 >      osw << "# selection: (" << selectionScript_ << ")\n";
406 >      osw << "# \n";
407 >      for (int l = 0; l <= lMax_; l++) {
408 >        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
409        }
410 +      // Normalize by number of frames and write it out:
411 +      for (int i = 0; i < nBins_; ++i) {
412 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
413 +        osw << Wval;
414 +        for (int l = 0; l <= lMax_; l++) {
415 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
416 +        }
417 +        osw << "\n";
418 +      }
419  
420 +      osw.close();
421 +    } else {
422 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
423 +              (getOutputFileName() + "w").c_str());
424 +      painCave.isFatal = 1;
425 +      simError();  
426      }
427 <
427 >      
428    }
429 <
429 > }

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