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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 3054 by gezelter, Wed Oct 18 21:58:48 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 1.19 2006-10-18 21:58:47 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_ = -0.25;
87 +    MaxW_ = 0.25;
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 +        // 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 <      DumpReader reader(info_, dumpFilename_);
149 <      int nFrames = reader.getNFrames();
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 <      /*Set the l for the spherical harmonic, it doesn't change*/
177 <      sphericalHarmonic.setL(lNumber_);
176 >    DumpReader reader(info_, dumpFilename_);    
177 >    int nFrames = reader.getNFrames();
178 >    frameCounter_ = 0;
179  
180 <      for (int i = 0; i < nFrames; i += step_) {
181 <        reader.readFrame(i);
182 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
183 <        nBonds = 0;
180 >    q_l.resize(lMax_+1);
181 >    q2.resize(lMax_+1);
182 >    w.resize(lMax_+1);
183 >    w_hat.resize(lMax_+1);
184  
185 <        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
186 <          //change the positions of atoms which belong to the rigidbodies
187 <          for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
188 <            rb->updateAtoms();
130 <          }
185 >    Q2.resize(lMax_+1);
186 >    Q.resize(lMax_+1);
187 >    W.resize(lMax_+1);
188 >    W_hat.resize(lMax_+1);
189  
190 <        }
190 >    for (int istep = 0; istep < nFrames; istep += step_) {
191 >      reader.readFrame(istep);
192 >      frameCounter_++;
193 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
194 >      
195 >      if (evaluator_.isDynamic()) {
196 >        seleMan_.setSelectionSet(evaluator_.evaluate());
197 >      }
198  
199 +      // update the positions of atoms which belong to the rigidbodies
200  
201 <        /* Setup QBar */
202 <        QBar_lm = new double[mSize_];
201 >      for (mol = info_->beginMolecule(mi); mol != NULL;
202 >           mol = info_->nextMolecule(mi)) {
203 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
204 >             rb = mol->nextRigidBody(rbIter)) {
205 >          rb->updateAtoms();
206 >        }        
207 >      }          
208 >            
209 >      // outer loop is over the selected StuntDoubles:
210  
211 <        /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
212 <        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));
211 >      for (sd = seleMan_.beginSelected(i); sd != NULL;
212 >           sd = seleMan_.nextSelected(i)) {
213  
214 <          /* Check to see if neighbor is in bond cuttoff*/
215 <          if (r<rCut_){
216 <            theta = atan(vec.y()/vec.x());
217 <            phi = acos(vec.z()/r);
218 <            for(int m_index = 0; m_index < mSize_; m_index++){
219 <              sphericalHarmonic.setM(m_index-lNumber_);
220 <              QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
221 <            }
222 <            nBonds++;
223 <          }
224 <        }
214 >        myIndex = sd->getGlobalIndex();
215 >        nBonds = 0;
216 >        
217 >        for (int l = 0; l <= lMax_; l++) {
218 >          for (int m = -l; m <= l; m++) {
219 >            q[std::make_pair(l,m)] = 0.0;
220 >          }
221 >        }
222 >        
223 >        // inner loop is over all other atoms in the system:
224 >        
225 >        for (mol = info_->beginMolecule(mi); mol != NULL;
226 >             mol = info_->nextMolecule(mi)) {
227 >          for (atom = mol->beginAtom(ai); atom != NULL;
228 >               atom = mol->nextAtom(ai)) {
229  
230 <        /*Normalize Qbar by number of Bonds*/
159 <        for ( int m_index = 0;m_index < mSize_; m_index++){
160 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
161 <        }
230 >            if (atom->getGlobalIndex() != myIndex) {
231  
232 +              vec = sd->getPos() - atom->getPos();      
233  
234 <      }
234 >              if (usePeriodicBoundaryConditions_)
235 >                currentSnapshot_->wrapVector(vec);
236 >              
237 >              // Calculate "bonds" and build Q_lm(r) where
238 >              //      Q_lm = Y_lm(theta(r),phi(r))                
239 >              // The spherical harmonics are wrt any arbitrary coordinate
240 >              // system, we choose standard spherical coordinates
241 >              
242 >              r = vec.length();
243 >              
244 >              // Check to see if neighbor is in bond cutoff
245 >              
246 >              if (r < rCut_) {
247 >                costheta = vec.z() / r;
248 >                phi = atan2(vec.y(), vec.x());
249  
250 <      /*Normalize by number of frames*/
251 <      for ( int m_index = 0;m_index < mSize_; m_index++){
252 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
253 <      }
250 >                for (int l = 0; l <= lMax_; l++) {
251 >                  sphericalHarmonic.setL(l);
252 >                  for(int m = -l; m <= l; m++){
253 >                    sphericalHarmonic.setM(m);
254 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
255 >                  }
256 >                }
257 >                nBonds++;
258 >              }  
259 >            }
260 >          }
261 >        }
262 >        
263 >        
264 >        for (int l = 0; l <= lMax_; l++) {        
265 >          q_l[l] = 0.0;
266 >          for(int m = -l; m <= l; m++) {
267 >            q_l[l] += norm(q[std::make_pair(l,m)]);
268 >          }    
269 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
270 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
271 >        }
272  
273 +        // Find second order invariant Q_l
274 +        
275 +        for (int l = 0; l <= lMax_; l++) {
276 +          q2[l] = 0.0;
277 +          for (int m = -l; m <= l; m++){
278 +            q2[l] += norm(q[std::make_pair(l,m)]);
279 +          }
280 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
281 +                        (RealType)(2*l + 1))/(RealType)nBonds;
282 +        }
283  
284 +        // Find Third Order Invariant W_l
285 +    
286 +        for (int l = 0; l <= lMax_; l++) {
287 +          w[l] = 0.0;
288 +          for (int m1 = -l; m1 <= l; m1++) {
289 +            std::pair<int,int> lm = std::make_pair(l, m1);
290 +            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
291 +              int m2 = m2Min[lm] + mmm;
292 +              int m3 = -m1-m2;
293 +              w[l] += w3j[lm][mmm] * q[lm] *
294 +                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
295 +            }
296 +          }
297 +          
298 +          w_hat[l] = w[l] / pow(q2[l], 1.5);
299 +        }
300  
301 <      /* Find second order invariant Q_l*/
302 <
303 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
304 <        QSq_l += pow(QBar_lm(m),2);
301 >        collectHistogram(q_l, w_hat);
302 >        
303 >        Nbonds += nBonds;
304 >        for (int l = 0; l <= lMax_;  l++) {
305 >          for (int m = -l; m <= l; m++) {
306 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
307 >          }
308 >        }
309        }
310 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
310 >    }
311 >      
312 >    // Normalize Qbar2
313 >    for (int l = 0; l <= lMax_; l++) {
314 >      for (int m = -l; m <= l; m++){
315 >        QBar[std::make_pair(l,m)] /= Nbonds;
316 >      }
317 >    }
318 >    
319 >    // Find second order invariant Q_l
320 >    
321 >    for (int l = 0; l <= lMax_; l++) {
322 >      Q2[l] = 0.0;
323 >      for (int m = -l; m <= l; m++){
324 >        Q2[l] += norm(QBar[std::make_pair(l,m)]);
325 >      }
326 >      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
327 >    }
328 >    
329 >    // Find Third Order Invariant W_l
330 >    
331 >    for (int l = 0; l <= lMax_; l++) {
332 >      W[l] = 0.0;
333 >      for (int m1 = -l; m1 <= l; m1++) {
334 >        std::pair<int,int> lm = std::make_pair(l, m1);
335 >        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
336 >          int m2 = m2Min[lm] + mmm;
337 >          int m3 = -m1-m2;
338 >          W[l] += w3j[lm][mmm] * QBar[lm] *
339 >            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
340 >        }
341 >      }
342 >      
343 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
344 >    }
345 >    
346 >    writeOrderParameter(Q, W_hat);    
347 >  }
348  
349 <      /* Find Third Order Invariant W_l*/
349 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
350 >                                            std::vector<ComplexType> what) {
351  
352 <      /* Make arrays for Wigner3jm */
353 <      double* THRCOF = new double[mSize_];
354 <      /* Variables for Wigner routine */
355 <      double l_ = (double)lNumber_;
356 <      double m2Min;
357 <      double m2Max;
358 <      int error;
359 <      int m1;
360 <      int m2;
361 <      int m3;
352 >    for (int l = 0; l <= lMax_; l++) {
353 >      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
354 >        int qbin = (q[l] - MinQ_) / deltaQ_;
355 >        Q_histogram_[std::make_pair(qbin,l)] += 1;
356 >        Qcount_[l]++;      
357 >      } else {
358 >        sprintf( painCave.errMsg,
359 >                 "q_l value outside reasonable range\n");
360 >        painCave.severity = OOPSE_ERROR;
361 >        painCave.isFatal = 1;
362 >        simError();  
363 >      }
364 >    }
365  
366 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
367 <        /* Zero work array */
368 <        for (i=0; i<mSize_;i++){
369 <          THRCOF[i] = 0.0;      
370 <        }
371 <        /* Get wigner coefficients */
372 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
373 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
374 <          m2 = floor(m2Min) + m_index - 1;
375 <          m3 = -m1-m2;
376 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
204 <        }
366 >    for (int l = 0; l <= lMax_; l++) {
367 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
368 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
369 >        W_histogram_[std::make_pair(wbin,l)] += 1;
370 >        Wcount_[l]++;      
371 >      } else {
372 >        sprintf( painCave.errMsg,
373 >                 "Re[w_hat] value outside reasonable range\n");
374 >        painCave.severity = OOPSE_ERROR;
375 >        painCave.isFatal = 1;
376 >        simError();  
377        }
378 +    }
379  
380 +  }  
381  
208 –      writeOrderParameter();
382  
383 <    }
383 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
384 >                                               std::vector<ComplexType> What) {
385 >    
386 >    std::ofstream osq((getOutputFileName() + "q").c_str());
387  
388 +    if (osq.is_open()) {
389 +      
390 +      osq << "# Bond Order Parameters\n";
391 +      osq << "# selection: (" << selectionScript_ << ")\n";
392 +      osq << "# \n";
393 +      for (int l = 0; l <= lMax_; l++) {
394 +        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
395 +      }
396 +      // Normalize by number of frames and write it out:
397 +      for (int i = 0; i < nBins_; ++i) {
398 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
399 +        osq << Qval;
400 +        for (int l = 0; l <= lMax_; l++) {
401 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
402 +            (RealType)Qcount_[l];
403 +        }
404 +        osq << "\n";
405 +      }
406  
407 <    void BondOrderParameter::writeOrderParameter() {
407 >      osq.close();
408  
409 <      std::ofstream os(getOutputFileName().c_str());
410 <      os << "#radial distribution function\n";
411 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
412 <      os << "selection2: (" << selectionScript2_ << ")\n";
413 <      os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
409 >    } else {
410 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
411 >              (getOutputFileName() + "q").c_str());
412 >      painCave.isFatal = 1;
413 >      simError();  
414 >    }
415  
416 <      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";
416 >    std::ofstream osw((getOutputFileName() + "w").c_str());
417  
418 +    if (osw.is_open()) {
419 +      osw << "# Bond Order Parameters\n";
420 +      osw << "# selection: (" << selectionScript_ << ")\n";
421 +      osw << "# \n";
422 +      for (int l = 0; l <= lMax_; l++) {
423 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
424        }
425 +      // Normalize by number of frames and write it out:
426 +      for (int i = 0; i < nBins_; ++i) {
427 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
428 +        osw << Wval;
429 +        for (int l = 0; l <= lMax_; l++) {
430 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
431 +            (RealType)Wcount_[l];
432 +        }
433 +        osw << "\n";
434 +      }
435  
436 +      osw.close();
437 +    } else {
438 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
439 +              (getOutputFileName() + "w").c_str());
440 +      painCave.isFatal = 1;
441 +      simError();  
442      }
443 <
443 >      
444    }
445 <
445 > }

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