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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 3087 by gezelter, Wed Dec 20 21:03:11 2006 UTC

# Line 37 | Line 37
37   * arising out of the use of or inability to use software, even if the
38   * University of Notre Dame has been advised of the possibility of
39   * such damages.
40 + *
41 + *  BondOrderParameter.cpp
42 + *  OOPSE-4
43 + *
44 + *  Created by J. Daniel Gezelter on 09/26/06.
45 + *  @author  J. Daniel Gezelter
46 + *  @version $Id: BondOrderParameter.cpp,v 1.22 2006-12-20 21:03:11 gezelter Exp $
47 + *
48   */
49 <
42 <
43 < /* Creates orientational bond order parameters as outlined by
44 < *     Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
45 < *     Phys Rev B, 28,784,1983
46 < *
47 < */
48 <
49 >
50   #include "applications/staticProps/BondOrderParameter.hpp"
51   #include "utils/simError.h"
52   #include "io/DumpReader.hpp"
53   #include "primitives/Molecule.hpp"
54   #include "utils/NumericConstant.hpp"
55 < #include "math/RealSphericalHarmonic.hpp"
55 >
56   namespace oopse {
57  
58 +  BondOrderParameter::BondOrderParameter(SimInfo* info,
59 +                                         const std::string& filename,
60 +                                         const std::string& sele,
61 +                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62 +    
63 +    setOutputName(getPrefix(filename) + ".bo");
64  
65 <  BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
66 <                                         const std::string& sele2, double rCut, int lNumber)
67 <    : StaticAnalyser(info, filename),
68 <      selectionScript1_(sele1), evaluator1_(info),
62 <      seleMan1_(info){
65 >    evaluator_.loadScriptString(sele);
66 >    if (!evaluator_.isDynamic()) {
67 >      seleMan_.setSelectionSet(evaluator_.evaluate());
68 >    }
69  
70 <    setOutputName(getPrefix(filename) + ".obo");
70 >    // Set up cutoff radius and order of the Legendre Polynomial:
71  
72 <    evaluator1_.loadScriptString(sele1);
73 <    evaluator2_.loadScriptString(sele2);
72 >    rCut_ = rCut;
73 >    nBins_ = nbins;
74 >    Qcount_.resize(lMax_+1);
75 >    Wcount_.resize(lMax_+1);
76  
77 <    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 <    }
77 >    // Q can take values from 0 to 1
78  
79 <    /* Set up cutoff radius and type of order parameter we are calcuating*/
80 <    lNumber_ = lNumber;
81 <    rCut_ = rCut;
82 <    mSize_ = 2*lNumber_+1;
79 >    MinQ_ = 0.0;
80 >    MaxQ_ = 1.1;
81 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
82  
83 <    int i;
84 <    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 <           }
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 +    MinW_ = -1.1;
87 +    MaxW_ = 1.1;
88 +    deltaW_ = (MaxW_ - MinW_) / nbins;
89  
90 <    }
90 >    // Make arrays for Wigner3jm
91 >    double* THRCOF = new double[2*lMax_+1];
92 >    // Variables for Wigner routine
93 >    double lPass, m1Pass, m2m, m2M;
94 >    int error, mSize;
95 >    mSize = 2*lMax_+1;
96  
97 <    void BondOrderParameter::process
98 <      () {
99 <      Molecule* mol;
100 <      RigidBody* rb;
102 <      SimInfo::MoleculeIterator mi;
103 <      Molecule::RigidBodyIterator rbIter;
104 <      RealType theta;
105 <      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;
97 >    for (int l = 0; l <= lMax_; l++) {
98 >      lPass = (double)l;
99 >      for (int m1 = -l; m1 <= l; m1++) {
100 >        m1Pass = (double)m1;
101  
102 +        std::pair<int,int> lm = std::make_pair(l, m1);
103 +        
104 +        // Zero work array
105 +        for (int ii = 0; ii < 2*l + 1; ii++){
106 +          THRCOF[ii] = 0.0;
107 +        }
108  
109 <      DumpReader reader(info_, dumpFilename_);
110 <      int nFrames = reader.getNFrames();
109 >        // Get Wigner coefficients
110 >        Wigner3jm(&lPass, &lPass, &lPass,
111 >                  &m1Pass, &m2m, &m2M,
112 >                  THRCOF, &mSize, &error);
113 >        
114 >        m2Min[lm] = (int)floor(m2m);
115 >        m2Max[lm] = (int)floor(m2M);
116 >        
117 >        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
118 >          w3j[lm].push_back(THRCOF[mmm]);
119 >        }
120 >      }
121 >    }
122 >    delete [] THRCOF;
123 >    THRCOF = NULL;
124 >  }
125 >  
126 >  BondOrderParameter::~BondOrderParameter() {
127 >    Q_histogram_.clear();
128 >    W_histogram_.clear();
129 >    for (int l = 0; l <= lMax_; l++) {
130 >      for (int m = -l; m <= l; m++) {
131 >        w3j[std::make_pair(l,m)].clear();
132 >      }
133 >    }
134 >    w3j.clear();
135 >    m2Min.clear();
136 >    m2Max.clear();
137 >  }
138 >  
139 >  void BondOrderParameter::initalizeHistogram() {
140 >    for (int bin = 0; bin < nBins_; bin++) {
141 >      for (int l = 0; l <= lMax_; l++) {
142 >        Q_histogram_[std::make_pair(bin,l)] = 0;
143 >        W_histogram_[std::make_pair(bin,l)] = 0;
144 >      }
145 >    }
146 >  }
147  
148 <      /*Set the l for the spherical harmonic, it doesn't change*/
149 <      sphericalHarmonic.setL(lNumber_);
148 >  void BondOrderParameter::process() {
149 >    Molecule* mol;
150 >    Atom* atom;
151 >    RigidBody* rb;
152 >    int myIndex;
153 >    SimInfo::MoleculeIterator mi;
154 >    Molecule::RigidBodyIterator rbIter;
155 >    Molecule::AtomIterator ai;
156 >    StuntDouble* sd;
157 >    Vector3d vec;
158 >    RealType costheta;
159 >    RealType phi;
160 >    RealType r;
161 >    RealType dist;
162 >    std::map<std::pair<int,int>,ComplexType> q;
163 >    std::vector<RealType> q_l;
164 >    std::vector<RealType> q2;
165 >    std::vector<ComplexType> w;
166 >    std::vector<ComplexType> w_hat;
167 >    std::map<std::pair<int,int>,ComplexType> QBar;
168 >    std::vector<RealType> Q2;
169 >    std::vector<RealType> Q;
170 >    std::vector<ComplexType> W;
171 >    std::vector<ComplexType> W_hat;
172 >    int nBonds, Nbonds;
173 >    SphericalHarmonic sphericalHarmonic;
174 >    int i, j;
175  
176 <      for (int i = 0; i < nFrames; i += step_) {
177 <        reader.readFrame(i);
178 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
124 <        nBonds = 0;
176 >    DumpReader reader(info_, dumpFilename_);    
177 >    int nFrames = reader.getNFrames();
178 >    frameCounter_ = 0;
179  
180 <        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
181 <          //change the positions of atoms which belong to the rigidbodies
182 <          for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
183 <            rb->updateAtoms();
130 <          }
180 >    q_l.resize(lMax_+1);
181 >    q2.resize(lMax_+1);
182 >    w.resize(lMax_+1);
183 >    w_hat.resize(lMax_+1);
184  
185 <        }
185 >    Q2.resize(lMax_+1);
186 >    Q.resize(lMax_+1);
187 >    W.resize(lMax_+1);
188 >    W_hat.resize(lMax_+1);
189 >    Nbonds = 0;
190  
191 +    for (int istep = 0; istep < nFrames; istep += step_) {
192 +      reader.readFrame(istep);
193 +      frameCounter_++;
194 +      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
195 +      
196 +      if (evaluator_.isDynamic()) {
197 +        seleMan_.setSelectionSet(evaluator_.evaluate());
198 +      }
199  
200 <        /* Setup QBar */
136 <        QBar_lm = new double[mSize_];
200 >      // update the positions of atoms which belong to the rigidbodies
201  
202 <        /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
203 <        for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
204 <          Vector3d vec = j->first->getPos() - j->second->getPos();
205 <          currentSnapshot_->wrapVector(vec);
206 <          /* The spherical harmonics are wrt any arbitray coordiate sysetm,
207 <           * we choose standard spherical coordinates */
208 <          r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
202 >      for (mol = info_->beginMolecule(mi); mol != NULL;
203 >           mol = info_->nextMolecule(mi)) {
204 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
205 >             rb = mol->nextRigidBody(rbIter)) {
206 >          rb->updateAtoms();
207 >        }        
208 >      }          
209 >            
210 >      // outer loop is over the selected StuntDoubles:
211  
212 <          /* Check to see if neighbor is in bond cuttoff*/
213 <          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 <        }
212 >      for (sd = seleMan_.beginSelected(i); sd != NULL;
213 >           sd = seleMan_.nextSelected(i)) {
214  
215 <        /*Normalize Qbar by number of Bonds*/
216 <        for ( int m_index = 0;m_index < mSize_; m_index++){
217 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
218 <        }
215 >        myIndex = sd->getGlobalIndex();
216 >        nBonds = 0;
217 >        
218 >        for (int l = 0; l <= lMax_; l++) {
219 >          for (int m = -l; m <= l; m++) {
220 >            q[std::make_pair(l,m)] = 0.0;
221 >          }
222 >        }
223 >        
224 >        // inner loop is over all other atoms in the system:
225 >        
226 >        for (mol = info_->beginMolecule(mi); mol != NULL;
227 >             mol = info_->nextMolecule(mi)) {
228 >          for (atom = mol->beginAtom(ai); atom != NULL;
229 >               atom = mol->nextAtom(ai)) {
230  
231 +            if (atom->getGlobalIndex() != myIndex) {
232  
233 <      }
233 >              vec = sd->getPos() - atom->getPos();      
234  
235 <      /*Normalize by number of frames*/
236 <      for ( int m_index = 0;m_index < mSize_; m_index++){
237 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
238 <      }
235 >              if (usePeriodicBoundaryConditions_)
236 >                currentSnapshot_->wrapVector(vec);
237 >              
238 >              // Calculate "bonds" and build Q_lm(r) where
239 >              //      Q_lm = Y_lm(theta(r),phi(r))                
240 >              // The spherical harmonics are wrt any arbitrary coordinate
241 >              // system, we choose standard spherical coordinates
242 >              
243 >              r = vec.length();
244 >              
245 >              // Check to see if neighbor is in bond cutoff
246 >              
247 >              if (r < rCut_) {
248 >                costheta = vec.z() / r;
249 >                phi = atan2(vec.y(), vec.x());
250  
251 +                for (int l = 0; l <= lMax_; l++) {
252 +                  sphericalHarmonic.setL(l);
253 +                  for(int m = -l; m <= l; m++){
254 +                    sphericalHarmonic.setM(m);
255 +                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256 +                  }
257 +                }
258 +                nBonds++;
259 +              }  
260 +            }
261 +          }
262 +        }
263 +        
264 +        
265 +        for (int l = 0; l <= lMax_; l++) {
266 +          q2[l] = 0.0;
267 +          for (int m = -l; m <= l; m++){
268 +            q[std::make_pair(l,m)] /= (RealType)nBonds;            
269 +            q2[l] += norm(q[std::make_pair(l,m)]);
270 +          }
271 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
272 +        }
273 +        
274 +        // Find Third Order Invariant W_l
275 +    
276 +        for (int l = 0; l <= lMax_; l++) {
277 +          w[l] = 0.0;
278 +          for (int m1 = -l; m1 <= l; m1++) {
279 +            std::pair<int,int> lm = std::make_pair(l, m1);
280 +            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
281 +              int m2 = m2Min[lm] + mmm;
282 +              int m3 = -m1-m2;
283 +              w[l] += w3j[lm][mmm] * q[lm] *
284 +                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
285 +            }
286 +          }
287 +          
288 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
289 +        }
290  
291 +        collectHistogram(q_l, w_hat);
292 +        
293 +        Nbonds += nBonds;
294 +        for (int l = 0; l <= lMax_;  l++) {
295 +          for (int m = -l; m <= l; m++) {
296 +            QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
297 +          }
298 +        }
299 +      }
300 +    }
301 +      
302 +    // Normalize Qbar2
303 +    for (int l = 0; l <= lMax_; l++) {
304 +      for (int m = -l; m <= l; m++){
305 +        QBar[std::make_pair(l,m)] /= Nbonds;
306 +      }
307 +    }
308 +    
309 +    // Find second order invariant Q_l
310 +    
311 +    for (int l = 0; l <= lMax_; l++) {
312 +      Q2[l] = 0.0;
313 +      for (int m = -l; m <= l; m++){
314 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
315 +      }
316 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317 +    }
318 +    
319 +    // Find Third Order Invariant W_l
320 +    
321 +    for (int l = 0; l <= lMax_; l++) {
322 +      W[l] = 0.0;
323 +      for (int m1 = -l; m1 <= l; m1++) {
324 +        std::pair<int,int> lm = std::make_pair(l, m1);
325 +        for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
326 +          int m2 = m2Min[lm] + mmm;
327 +          int m3 = -m1-m2;
328 +          W[l] += w3j[lm][mmm] * QBar[lm] *
329 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
330 +        }
331 +      }
332 +      
333 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
334 +    }
335 +    
336 +    writeOrderParameter(Q, W_hat);    
337 +  }
338  
339 <      /* Find second order invariant Q_l*/
339 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340 >                                            std::vector<ComplexType> what) {
341  
342 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
343 <        QSq_l += pow(QBar_lm(m),2);
342 >    for (int l = 0; l <= lMax_; l++) {
343 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344 >        int qbin = (q[l] - MinQ_) / deltaQ_;
345 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
346 >        Qcount_[l]++;      
347 >      } else {
348 >        sprintf( painCave.errMsg,
349 >                 "q_l value outside reasonable range\n");
350 >        painCave.severity = OOPSE_ERROR;
351 >        painCave.isFatal = 1;
352 >        simError();  
353        }
354 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
354 >    }
355  
356 <      /* Find Third Order Invariant W_l*/
356 >    for (int l = 0; l <= lMax_; l++) {
357 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
359 >        W_histogram_[std::make_pair(wbin,l)] += 1;
360 >        Wcount_[l]++;      
361 >      } else {
362 >        sprintf( painCave.errMsg,
363 >                 "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
364 >        painCave.severity = OOPSE_ERROR;
365 >        painCave.isFatal = 1;
366 >        simError();  
367 >      }
368 >    }
369  
370 <      /* 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;
370 >  }  
371  
372 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
373 <        /* Zero work array */
374 <        for (i=0; i<mSize_;i++){
375 <          THRCOF[i] = 0.0;      
376 <        }
377 <        /* Get wigner coefficients */
378 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
379 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
380 <          m2 = floor(m2Min) + m_index - 1;
381 <          m3 = -m1-m2;
382 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
383 <        }
372 >
373 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374 >                                               std::vector<ComplexType> What) {
375 >    
376 >    std::ofstream osq((getOutputFileName() + "q").c_str());
377 >
378 >    if (osq.is_open()) {
379 >      
380 >      osq << "# Bond Order Parameters\n";
381 >      osq << "# selection: (" << selectionScript_ << ")\n";
382 >      osq << "# \n";
383 >      for (int l = 0; l <= lMax_; l++) {
384 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385        }
386 +      // Normalize by number of frames and write it out:
387 +      for (int i = 0; i < nBins_; ++i) {
388 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
389 +        osq << Qval;
390 +        for (int l = 0; l <= lMax_; l++) {
391  
392 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393 +        }
394 +        osq << "\n";
395 +      }
396  
397 <      writeOrderParameter();
397 >      osq.close();
398  
399 +    } else {
400 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401 +              (getOutputFileName() + "q").c_str());
402 +      painCave.isFatal = 1;
403 +      simError();  
404      }
405  
406 +    std::ofstream osw((getOutputFileName() + "w").c_str());
407  
408 <    void BondOrderParameter::writeOrderParameter() {
408 >    if (osw.is_open()) {
409 >      osw << "# Bond Order Parameters\n";
410 >      osw << "# selection: (" << selectionScript_ << ")\n";
411 >      osw << "# \n";
412 >      for (int l = 0; l <= lMax_; l++) {
413 >        osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
414 >      }
415 >      // Normalize by number of frames and write it out:
416 >      for (int i = 0; i < nBins_; ++i) {
417 >        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
418 >        osw << Wval;
419 >        for (int l = 0; l <= lMax_; l++) {
420  
421 <      std::ofstream os(getOutputFileName().c_str());
422 <      os << "#radial distribution function\n";
423 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
218 <      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 <
421 >          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422 >        }
423 >        osw << "\n";
424        }
425  
426 +      osw.close();
427 +    } else {
428 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
429 +              (getOutputFileName() + "w").c_str());
430 +      painCave.isFatal = 1;
431 +      simError();  
432      }
433 <
433 >      
434    }
435 <
435 > }

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