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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40 + *
41 + *  Created by J. Daniel Gezelter on 09/26/06.
42 + *  @author  J. Daniel Gezelter
43 + *  @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $
44 + *
45   */
41 –
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 – */
46  
47   #include "applications/staticProps/BondOrderParameter.hpp"
48   #include "utils/simError.h"
49   #include "io/DumpReader.hpp"
50   #include "primitives/Molecule.hpp"
51   #include "utils/NumericConstant.hpp"
54 – #include "math/RealSphericalHarmonic.hpp"
55 – namespace oopse {
52  
53 + namespace OpenMD {
54  
55    BondOrderParameter::BondOrderParameter(SimInfo* info,
56                                           const std::string& filename,
57                                           const std::string& sele,
58 <                                         double rCut, int lNumber, int nbins)
62 <    : StaticAnalyser(info, filename), selectionScript_(sele),
63 <      evaluator_(info), seleMan_(info){
58 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
59      
60 <    setOutputName(getPrefix(filename) + ".obo");
60 >    setOutputName(getPrefix(filename) + ".bo");
61  
62      evaluator_.loadScriptString(sele);
63      if (!evaluator_.isDynamic()) {
# Line 71 | Line 66 | namespace oopse {
66  
67      // Set up cutoff radius and order of the Legendre Polynomial:
68  
74 –    lNumber_ = lNumber;
69      rCut_ = rCut;
70 <    mSize_ = 2*lNumber_+1;    
70 >    nBins_ = nbins;
71 >    Qcount_.resize(lMax_+1);
72 >    Wcount_.resize(lMax_+1);
73  
74 <    // Set the l for the spherical harmonic, it doesn't change
74 >    // Q can take values from 0 to 1
75  
76 <    sphericalHarmonic.setL(lNumber_);
76 >    MinQ_ = 0.0;
77 >    MaxQ_ = 1.1;
78 >    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
79  
80 <    delta_Q = 1.0 / nbins;
81 <    delta_W = 2.0 / nbins;
80 >    // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
81 >    // use values for MinW_ and MaxW_ that are slightly larger than this:
82  
83 <    Q_histogram_.resize(nbins);
84 <    W_histogram_.resize(nbins);
83 >    MinW_ = -1.1;
84 >    MaxW_ = 1.1;
85 >    deltaW_ = (MaxW_ - MinW_) / nbins;
86  
87 <  }
87 >    // Make arrays for Wigner3jm
88 >    double* THRCOF = new double[2*lMax_+1];
89 >    // Variables for Wigner routine
90 >    double lPass, m1Pass, m2m, m2M;
91 >    int error, mSize;
92 >    mSize = 2*lMax_+1;
93  
94 +    for (int l = 0; l <= lMax_; l++) {
95 +      lPass = (double)l;
96 +      for (int m1 = -l; m1 <= l; m1++) {
97 +        m1Pass = (double)m1;
98 +
99 +        std::pair<int,int> lm = std::make_pair(l, m1);
100 +        
101 +        // Zero work array
102 +        for (int ii = 0; ii < 2*l + 1; ii++){
103 +          THRCOF[ii] = 0.0;
104 +        }
105 +
106 +        // Get Wigner coefficients
107 +        Wigner3jm(&lPass, &lPass, &lPass,
108 +                  &m1Pass, &m2m, &m2M,
109 +                  THRCOF, &mSize, &error);
110 +        
111 +        m2Min[lm] = (int)floor(m2m);
112 +        m2Max[lm] = (int)floor(m2M);
113 +        
114 +        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
115 +          w3j[lm].push_back(THRCOF[mmm]);
116 +        }
117 +      }
118 +    }
119 +    delete [] THRCOF;
120 +    THRCOF = NULL;
121 +  }
122 +  
123 +  BondOrderParameter::~BondOrderParameter() {
124 +    Q_histogram_.clear();
125 +    W_histogram_.clear();
126 +    for (int l = 0; l <= lMax_; l++) {
127 +      for (int m = -l; m <= l; m++) {
128 +        w3j[std::make_pair(l,m)].clear();
129 +      }
130 +    }
131 +    w3j.clear();
132 +    m2Min.clear();
133 +    m2Max.clear();
134 +  }
135 +  
136    void BondOrderParameter::initalizeHistogram() {
137 <    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
138 <    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
137 >    for (int bin = 0; bin < nBins_; bin++) {
138 >      for (int l = 0; l <= lMax_; l++) {
139 >        Q_histogram_[std::make_pair(bin,l)] = 0;
140 >        W_histogram_[std::make_pair(bin,l)] = 0;
141 >      }
142 >    }
143    }
144  
145    void BondOrderParameter::process() {
146      Molecule* mol;
147      Atom* atom;
148      RigidBody* rb;
149 +    int myIndex;
150      SimInfo::MoleculeIterator mi;
151      Molecule::RigidBodyIterator rbIter;
152      Molecule::AtomIterator ai;
153      StuntDouble* sd;
154 <    RealType theta;
154 >    Vector3d vec;
155 >    RealType costheta;
156      RealType phi;
157      RealType r;
158      RealType dist;
159 <    std::map<int, RealType> QBar_lm;
160 <    RealType QSq_l;
161 <    RealType Q_l;
162 <    int nBonds;
163 <    RealSphericalHarmonic sphericalHarmonic;
159 >    std::map<std::pair<int,int>,ComplexType> q;
160 >    std::vector<RealType> q_l;
161 >    std::vector<RealType> q2;
162 >    std::vector<ComplexType> w;
163 >    std::vector<ComplexType> w_hat;
164 >    std::map<std::pair<int,int>,ComplexType> QBar;
165 >    std::vector<RealType> Q2;
166 >    std::vector<RealType> Q;
167 >    std::vector<ComplexType> W;
168 >    std::vector<ComplexType> W_hat;
169 >    int nBonds, Nbonds;
170 >    SphericalHarmonic sphericalHarmonic;
171      int i, j;
172 <  
114 <  
172 >
173      DumpReader reader(info_, dumpFilename_);    
174      int nFrames = reader.getNFrames();
175 +    frameCounter_ = 0;
176  
177 +    q_l.resize(lMax_+1);
178 +    q2.resize(lMax_+1);
179 +    w.resize(lMax_+1);
180 +    w_hat.resize(lMax_+1);
181  
182 +    Q2.resize(lMax_+1);
183 +    Q.resize(lMax_+1);
184 +    W.resize(lMax_+1);
185 +    W_hat.resize(lMax_+1);
186 +    Nbonds = 0;
187 +
188      for (int istep = 0; istep < nFrames; istep += step_) {
189        reader.readFrame(istep);
190 +      frameCounter_++;
191        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
192        
193        if (evaluator_.isDynamic()) {
# Line 132 | Line 202 | namespace oopse {
202               rb = mol->nextRigidBody(rbIter)) {
203            rb->updateAtoms();
204          }        
205 <      }      
206 <      
205 >      }          
206 >            
207        // outer loop is over the selected StuntDoubles:
208  
209        for (sd = seleMan_.beginSelected(i); sd != NULL;
210             sd = seleMan_.nextSelected(i)) {
211  
212 <        // For this central atom, zero out nBonds and QBar_lm
143 <
212 >        myIndex = sd->getGlobalIndex();
213          nBonds = 0;
214 <      
215 <        for (int m = -lNumber_; m <= lNumber_; m++) {
216 <          QBar_lm[m] = 0.0;
214 >        
215 >        for (int l = 0; l <= lMax_; l++) {
216 >          for (int m = -l; m <= l; m++) {
217 >            q[std::make_pair(l,m)] = 0.0;
218 >          }
219          }
220          
221          // inner loop is over all other atoms in the system:
# Line 154 | Line 225 | namespace oopse {
225            for (atom = mol->beginAtom(ai); atom != NULL;
226                 atom = mol->nextAtom(ai)) {
227  
228 +            if (atom->getGlobalIndex() != myIndex) {
229  
230 <            Vector3d vec = sd->getPos() - atom->getPos();      
231 <            currentSnapshot_->wrapVector(vec);
232 <            
233 <            // Calculate "bonds" and build Q_lm(r) where
234 <            //      Q_lm = Y_lm(theta(r),phi(r))                
235 <            // The spherical harmonics are wrt any arbitrary coordinate
236 <            // system, we choose standard spherical coordinates
237 <            
238 <            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
239 <            
240 <            // Check to see if neighbor is in bond cutoff
241 <            
242 <            if (r < rCut_) {            
243 <              theta = atan2(vec.y(), vec.x());
244 <              phi = acos(vec.z()/r);
245 <              for(int m = -lNumber_; m <= lNumber_; m++){
246 <                sphericalHarmonic.setM(m);
247 <                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
248 <              }
249 <              nBonds++;
250 <            }  
230 >              vec = sd->getPos() - atom->getPos();      
231 >
232 >              if (usePeriodicBoundaryConditions_)
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 >                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 <        // Normalize Qbar
262 <        for (int m = -lNumber_;m <= lNumber_; m++){
263 <          QBar_lm[m] /= nBonds;
261 >        
262 >        for (int l = 0; l <= lMax_; l++) {
263 >          q2[l] = 0.0;
264 >          for (int m = -l; m <= l; m++){
265 >            q[std::make_pair(l,m)] /= (RealType)nBonds;            
266 >            q2[l] += norm(q[std::make_pair(l,m)]);
267 >          }
268 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
269          }
270 <
187 <        // Find second order invariant Q_l
188 <
189 <        QSq_l = 0.0;
190 <        for (int m = -lNumber_; m <= lNumber_; m++){
191 <          QSq_l += pow(QBar_lm[m], 2);  
192 <        }
193 <        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
194 <    
270 >        
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 <        // Make arrays for Wigner3jm
198 <        double* THRCOF = new double[mSize_];
199 <        // Variables for Wigner routine
200 <        double l_ = (double)lNumber_;
201 <        double m2Min, m2Max;
202 <        int error, m1, m2, m3;
288 >        collectHistogram(q_l, w_hat);
289          
290 <        W_l_ = 0.0;
291 <        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
292 <          // Zero work array
293 <          for (int ii = 0; ii < mSize_; ii+){
208 <            THRCOF[i] = 0.0;
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)] += (RealType)nBonds*q[std::make_pair(l,m)];
294            }
210 –          // Get Wigner coefficients
211 –          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
212 –          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
213 –            m2 = floor(m2Min) + m_index - 1;
214 –            m3 = -m1-m2;
215 –            W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
216 –          }
295          }
218 –
219 –        W_l_hat = W_l_ / pow(QSq_l, 1.5);
220 –
221 –        // accumulate histogram data for Q_l and W_l_hat:
222 –
223 –        collectHistogram(Q_l, W_l_hat);
224 –                
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 <    // Normalize by number of frames
307 <    for (int m = -lNumber_; m <= lNumber_; m++){
308 <      QBar_lm[m] /=  nFrames;  
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 <    
234 <    
235 <    
236 <    
237 <    writeOrderParameter();
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 <  
337 <  void BondOrderParameter::processHistogram() {
243 <    
244 <    int nPairs = getNPairs();
245 <    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
246 <    RealType pairDensity = nPairs /volume * 2.0;
247 <    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
336 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 >                                            std::vector<ComplexType> what) {
338  
339 <    for(int i = 0 ; i < histogram_.size(); ++i){
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 = OPENMD_ERROR;
348 >        painCave.isFatal = 1;
349 >        simError();  
350 >      }
351 >    }
352  
353 <      RealType rLower = i * deltaR_;
354 <      RealType rUpper = rLower + deltaR_;
355 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
356 <      RealType nIdeal = volSlice * pairConstant;
357 <
358 <      avgGofr_[i] += histogram_[i] / nIdeal;    
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 (%lf) outside reasonable range\n", real(what[l]));
361 >        painCave.severity = OPENMD_ERROR;
362 >        painCave.isFatal = 1;
363 >        simError();  
364 >      }
365      }
366  
367 <  }
367 >  }  
368  
261 –  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
369  
370 <    if (Q_l < Max_Q) {
371 <      int whichBin = Q_l / deltaQ_;
372 <      Q_histogram_[whichBin] += 1;
373 <    }
267 <    if (W_l_hat < Max_W) {
268 <      int whichBin = W_l_hat / deltaW_;
269 <      W_histogram_[whichBin] += 1;
270 <    }
271 <  }
272 <  
370 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 >                                               std::vector<ComplexType> What) {
372 >    
373 >    std::ofstream osq((getOutputFileName() + "q").c_str());
374  
375 <  void BondOrderParameter::writeOrderParameter() {
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  
389 <    std::ofstream os(getOutputFileName().c_str());
390 <    os << "#Bond Order Parameter\n";
391 <    os << "#selection: (" << selectionScript_ << ")\n";
389 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
390 >        }
391 >        osq << "\n";
392 >      }
393  
394 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
281 <      os <<  orderParams_[i].p2 << "\t"
282 <         <<  orderParams_[i].director[0] << "\t"
283 <         <<  orderParams_[i].director[1] << "\t"
284 <         <<  orderParams_[i].director[2] << "\t"
285 <         <<  orderParams_[i].angle << "\n";
394 >      osq.close();
395  
396 +    } else {
397 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
398 +              (getOutputFileName() + "q").c_str());
399 +      painCave.isFatal = 1;
400 +      simError();  
401      }
288 –  }
402  
403 +    std::ofstream osw((getOutputFileName() + "w").c_str());
404  
405 +    if (osw.is_open()) {
406 +      osw << "# Bond Order Parameters\n";
407 +      osw << "# selection: (" << selectionScript_ << ")\n";
408 +      osw << "# \n";
409 +      for (int l = 0; l <= lMax_; l++) {
410 +        osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
411 +      }
412 +      // Normalize by number of frames and write it out:
413 +      for (int i = 0; i < nBins_; ++i) {
414 +        RealType Wval = MinW_ + (i + 0.5) * deltaW_;              
415 +        osw << Wval;
416 +        for (int l = 0; l <= lMax_; l++) {
417  
418 +          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
419 +        }
420 +        osw << "\n";
421 +      }
422 +
423 +      osw.close();
424 +    } else {
425 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
426 +              (getOutputFileName() + "w").c_str());
427 +      painCave.isFatal = 1;
428 +      simError();  
429 +    }
430 +      
431 +  }
432   }

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