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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 3026 by gezelter, Tue Sep 26 16:08:44 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 1.18 2006-09-26 16:08:44 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 +    // 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 +    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 <    void BondOrderParameter::process
149 <      () {
150 <      Molecule* mol;
151 <      RigidBody* rb;
152 <      SimInfo::MoleculeIterator mi;
153 <      Molecule::RigidBodyIterator rbIter;
154 <      RealType theta;
155 <      RealType phi;
156 <      RealType r;
157 <      RealType dist;
158 <      RealType* QBar_lm;
159 <      RealType QSq_l;
160 <      int nBonds;
161 <      int m, m_index;
162 <      RealSphericalHarmonic sphericalHarmonic;
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 +    DumpReader reader(info_, dumpFilename_);    
177 +    int nFrames = reader.getNFrames();
178 +    frameCounter_ = 0;
179  
180 <      DumpReader reader(info_, dumpFilename_);
181 <      int nFrames = reader.getNFrames();
180 >    q_l.resize(lMax_+1);
181 >    q2.resize(lMax_+1);
182 >    w.resize(lMax_+1);
183 >    w_hat.resize(lMax_+1);
184  
185 <      /*Set the l for the spherical harmonic, it doesn't change*/
186 <      sphericalHarmonic.setL(lNumber_);
185 >    Q2.resize(lMax_+1);
186 >    Q.resize(lMax_+1);
187 >    W.resize(lMax_+1);
188 >    W_hat.resize(lMax_+1);
189  
190 <      for (int i = 0; i < nFrames; i += step_) {
191 <        reader.readFrame(i);
192 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
193 <        nBonds = 0;
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 <        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 <          }
199 >      // update the positions of atoms which belong to the rigidbodies
200  
201 <        }
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 +      for (sd = seleMan_.beginSelected(i); sd != NULL;
212 +           sd = seleMan_.nextSelected(i)) {
213  
214 <        /* Setup QBar */
215 <        QBar_lm = new double[mSize_];
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 <        /* 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));
230 >            if (atom->getGlobalIndex() != myIndex) {
231  
232 <          /* Check to see if neighbor is in bond cuttoff*/
233 <          if (r<rCut_){
234 <            theta = atan(vec.y()/vec.x());
235 <            phi = acos(vec.z()/r);
236 <            for(int m_index = 0; m_index < mSize_; m_index++){
237 <              sphericalHarmonic.setM(m_index-lNumber_);
238 <              QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
239 <            }
240 <            nBonds++;
241 <          }
242 <        }
232 >              vec = sd->getPos() - atom->getPos();      
233 >              currentSnapshot_->wrapVector(vec);
234 >              
235 >              // Calculate "bonds" and build Q_lm(r) where
236 >              //      Q_lm = Y_lm(theta(r),phi(r))                
237 >              // The spherical harmonics are wrt any arbitrary coordinate
238 >              // system, we choose standard spherical coordinates
239 >              
240 >              r = vec.length();
241 >              
242 >              // Check to see if neighbor is in bond cutoff
243 >              
244 >              if (r < rCut_) {
245 >                costheta = vec.z() / r;
246 >                phi = atan2(vec.y(), vec.x());
247  
248 <        /*Normalize Qbar by number of Bonds*/
249 <        for ( int m_index = 0;m_index < mSize_; m_index++){
250 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
251 <        }
248 >                for (int l = 0; l <= lMax_; l++) {
249 >                  sphericalHarmonic.setL(l);
250 >                  for(int m = -l; m <= l; m++){
251 >                    sphericalHarmonic.setM(m);
252 >                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
253 >                  }
254 >                }
255 >                nBonds++;
256 >              }  
257 >            }
258 >          }
259 >        }
260 >        
261 >        
262 >        for (int l = 0; l <= lMax_; l++) {        
263 >          q_l[l] = 0.0;
264 >          for(int m = -l; m <= l; m++) {
265 >            q_l[l] += norm(q[std::make_pair(l,m)]);
266 >          }    
267 >          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
268 >          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
269 >        }
270  
271 +        // Find second order invariant Q_l
272 +        
273 +        for (int l = 0; l <= lMax_; l++) {
274 +          q2[l] = 0.0;
275 +          for (int m = -l; m <= l; m++){
276 +            q2[l] += norm(q[std::make_pair(l,m)]);
277 +          }
278 +          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
279 +                        (RealType)(2*l + 1))/(RealType)nBonds;
280 +        }
281  
282 <      }
282 >        // Find Third Order Invariant W_l
283 >    
284 >        for (int l = 0; l <= lMax_; l++) {
285 >          w[l] = 0.0;
286 >          for (int m1 = -l; m1 <= l; m1++) {
287 >            std::pair<int,int> lm = std::make_pair(l, m1);
288 >            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
289 >              int m2 = m2Min[lm] + mmm;
290 >              int m3 = -m1-m2;
291 >              w[l] += w3j[lm][mmm] * q[lm] *
292 >                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
293 >            }
294 >          }
295 >          
296 >          w_hat[l] = w[l] / pow(q2[l], 1.5);
297 >        }
298  
299 <      /*Normalize by number of frames*/
300 <      for ( int m_index = 0;m_index < mSize_; m_index++){
301 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
299 >        collectHistogram(q_l, w_hat);
300 >        
301 >        Nbonds += nBonds;
302 >        for (int l = 0; l <= lMax_;  l++) {
303 >          for (int m = -l; m <= l; m++) {
304 >            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
305 >          }
306 >        }
307        }
308 +    }
309 +      
310 +    // Normalize Qbar2
311 +    for (int l = 0; l <= lMax_; l++) {
312 +      for (int m = -l; m <= l; m++){
313 +        QBar[std::make_pair(l,m)] /= Nbonds;
314 +      }
315 +    }
316 +    
317 +    // Find second order invariant Q_l
318 +    
319 +    for (int l = 0; l <= lMax_; l++) {
320 +      Q2[l] = 0.0;
321 +      for (int m = -l; m <= l; m++){
322 +        Q2[l] += norm(QBar[std::make_pair(l,m)]);
323 +      }
324 +      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
325 +    }
326 +    
327 +    // Find Third Order Invariant W_l
328 +    
329 +    for (int l = 0; l <= lMax_; l++) {
330 +      W[l] = 0.0;
331 +      for (int m1 = -l; m1 <= l; m1++) {
332 +        std::pair<int,int> lm = std::make_pair(l, m1);
333 +        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
334 +          int m2 = m2Min[lm] + mmm;
335 +          int m3 = -m1-m2;
336 +          W[l] += w3j[lm][mmm] * QBar[lm] *
337 +            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
338 +        }
339 +      }
340 +      
341 +      W_hat[l] = W[l] / pow(Q2[l], 1.5);
342 +    }
343 +    
344 +    writeOrderParameter(Q, W_hat);    
345 +  }
346  
347 +  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
348 +                                            std::vector<ComplexType> what) {
349  
350 +    for (int l = 0; l <= lMax_; l++) {
351 +      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
352 +        int qbin = (q[l] - MinQ_) / deltaQ_;
353 +        Q_histogram_[std::make_pair(qbin,l)] += 1;
354 +        Qcount_[l]++;      
355 +      } else {
356 +        sprintf( painCave.errMsg,
357 +                 "q_l value outside reasonable range\n");
358 +        painCave.severity = OOPSE_ERROR;
359 +        painCave.isFatal = 1;
360 +        simError();  
361 +      }
362 +    }
363  
364 <      /* Find second order invariant Q_l*/
365 <
366 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
367 <        QSq_l += pow(QBar_lm(m),2);
364 >    for (int l = 0; l <= lMax_; l++) {
365 >      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
366 >        int wbin = (real(what[l]) - MinW_) / deltaW_;
367 >        W_histogram_[std::make_pair(wbin,l)] += 1;
368 >        Wcount_[l]++;      
369 >      } else {
370 >        sprintf( painCave.errMsg,
371 >                 "Re[w_hat] value outside reasonable range\n");
372 >        painCave.severity = OOPSE_ERROR;
373 >        painCave.isFatal = 1;
374 >        simError();  
375        }
376 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
376 >    }
377  
378 <      /* Find Third Order Invariant W_l*/
378 >  }  
379  
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;
380  
381 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
382 <        /* Zero work array */
383 <        for (i=0; i<mSize_;i++){
384 <          THRCOF[i] = 0.0;      
385 <        }
386 <        /* Get wigner coefficients */
387 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
388 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
389 <          m2 = floor(m2Min) + m_index - 1;
390 <          m3 = -m1-m2;
391 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
392 <        }
381 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
382 >                                               std::vector<ComplexType> What) {
383 >    
384 >    std::ofstream osq((getOutputFileName() + "q").c_str());
385 >
386 >    if (osq.is_open()) {
387 >      
388 >      osq << "# Bond Order Parameters\n";
389 >      osq << "# selection: (" << selectionScript_ << ")\n";
390 >      osq << "# \n";
391 >      for (int l = 0; l <= lMax_; l++) {
392 >        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
393        }
394 +      // Normalize by number of frames and write it out:
395 +      for (int i = 0; i < nBins_; ++i) {
396 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
397 +        osq << Qval;
398 +        for (int l = 0; l <= lMax_; l++) {
399 +          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
400 +            (RealType)Qcount_[l];
401 +        }
402 +        osq << "\n";
403 +      }
404  
405 +      osq.close();
406  
407 <      writeOrderParameter();
408 <
407 >    } else {
408 >      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
409 >              (getOutputFileName() + "q").c_str());
410 >      painCave.isFatal = 1;
411 >      simError();  
412      }
413  
414 +    std::ofstream osw((getOutputFileName() + "w").c_str());
415  
416 <    void BondOrderParameter::writeOrderParameter() {
417 <
418 <      std::ofstream os(getOutputFileName().c_str());
419 <      os << "#radial distribution function\n";
420 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
421 <      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 <
416 >    if (osw.is_open()) {
417 >      osw << "# Bond Order Parameters\n";
418 >      osw << "# selection: (" << selectionScript_ << ")\n";
419 >      osw << "# \n";
420 >      for (int l = 0; l <= lMax_; l++) {
421 >        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
422        }
423 +      // Normalize by number of frames and write it out:
424 +      for (int i = 0; i < nBins_; ++i) {
425 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
426 +        osw << Wval;
427 +        for (int l = 0; l <= lMax_; l++) {
428 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
429 +            (RealType)Wcount_[l];
430 +        }
431 +        osw << "\n";
432 +      }
433  
434 +      osw.close();
435 +    } else {
436 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
437 +              (getOutputFileName() + "w").c_str());
438 +      painCave.isFatal = 1;
439 +      simError();  
440      }
441 <
441 >      
442    }
443 <
443 > }

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