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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1049 by gezelter, Fri Sep 22 01:41:11 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/SphericalHarmonic.hpp"
52  
53 < namespace oopse {
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) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
58 >                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
59      
60      setOutputName(getPrefix(filename) + ".bo");
61  
# Line 69 | Line 66 | namespace oopse {
66  
67      // Set up cutoff radius and order of the Legendre Polynomial:
68  
72 –    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      // Q can take values from 0 to 1
75  
76      MinQ_ = 0.0;
77 <    MaxQ_ = 3.0;
77 >    MaxQ_ = 1.1;
78      deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81 –    Q_histogram_.resize(nbins);
79  
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 <    MinW_ = -0.18;
84 <    MaxW_ = 0.18;
83 >    MinW_ = -1.1;
84 >    MaxW_ = 1.1;
85      deltaW_ = (MaxW_ - MinW_) / nbins;
89 –    W_histogram_.resize(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 <
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() {
# Line 114 | Line 156 | namespace oopse {
156      RealType phi;
157      RealType r;
158      RealType dist;
159 <    std::map<int,ComplexType> q_lm;
160 <    std::map<int,ComplexType> QBar_lm;
161 <    RealType QSq_l;
162 <    RealType Q_l;
163 <    ComplexType W_l;
164 <    ComplexType W_l_hat;
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;
126 –    // Make arrays for Wigner3jm
127 –    double* THRCOF = new double[mSize_];
128 –    // Variables for Wigner routine
129 –    double l_ = (double)lNumber_;
130 –    double m1Pass, m2Min, m2Max;
131 –    int error, m1, m2, m3;
172  
133 –    // Set the l for the spherical harmonic, it doesn't change
134 –    sphericalHarmonic.setL(lNumber_);
135 –
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_++;
# Line 163 | Line 211 | namespace oopse {
211  
212          myIndex = sd->getGlobalIndex();
213          nBonds = 0;
214 <        for (int m = -lNumber_; m <= lNumber_; m++) {
215 <          q_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 177 | Line 228 | namespace oopse {
228              if (atom->getGlobalIndex() != myIndex) {
229  
230                vec = sd->getPos() - atom->getPos();      
231 <              currentSnapshot_->wrapVector(vec);
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))                
# Line 191 | Line 244 | namespace oopse {
244                if (r < rCut_) {
245                  costheta = vec.z() / r;
246                  phi = atan2(vec.y(), vec.x());
247 <                
248 <                for(int m = -lNumber_; m <= lNumber_; m++){
249 <                  sphericalHarmonic.setM(m);
250 <                  q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
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 <        RealType ql = 0.0;
261 <        for(int m=-lNumber_; m<=lNumber_; m++) {          
262 <          ql += norm(QBar_lm[m]);
263 <        }        
264 <        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
265 <        collectHistogram(sqrt(ql)/(RealType)nBonds);
260 >        
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 >        
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 +        collectHistogram(q_l, w_hat);
289 +        
290          Nbonds += nBonds;
291 <        for (int m=-lNumber_; m<=lNumber_; m++) {
292 <          QBar_lm[m] += q_lm[m];
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 >          }
295          }
296        }
297      }
298 <
298 >      
299      // Normalize Qbar2
300 <    for (int m = -lNumber_;m <= lNumber_; m++){
301 <      QBar_lm[m] /= Nbonds;
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      // Find second order invariant Q_l
307      
308 <    QSq_l = 0.0;
309 <    for (int m = -lNumber_; m <= lNumber_; m++){
310 <      QSq_l += norm(QBar_lm[m]);
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      
230 –    std::cout << "qsl = " << QSq_l << "\n";
231 –    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
232 –    
316      // Find Third Order Invariant W_l
317      
318 <    W_l = 0.0;
319 <    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
320 <      // Zero work array
321 <      for (int ii = 0; ii < mSize_; ii++){
322 <        THRCOF[ii] = 0.0;
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        }
241 –      // Get Wigner coefficients
242 –      m1Pass = (double)m1;
329        
330 <      Wigner3jm(&l_, &l_, &l_,
245 <                &m1Pass, &m2Min, &m2Max,
246 <                THRCOF, &mSize_, &error);
247 <      
248 <      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
249 <        m2 = (int)floor(m2Min) + mmm;
250 <        m3 = -m1-m2;
251 <        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
252 <      }
330 >      W_hat[l] = W[l] / pow(Q2[l], 1.5);
331      }
332      
333 <    W_l_hat = W_l / pow(QSq_l, 1.5);              
256 <    
257 <    writeOrderParameter(Q_l, real(W_l_hat));    
333 >    writeOrderParameter(Q, W_hat);    
334    }
335  
336 <  void BondOrderParameter::collectHistogram(RealType q_l) {
336 >  void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337 >                                            std::vector<ComplexType> what) {
338  
339 <    if (q_l >= MinQ_ && q_l < MaxQ_) {
340 <      int qbin = (q_l - MinQ_) / deltaQ_;
341 <      Q_histogram_[qbin] += 1;
342 <      Qcount_++;
343 <      sumQ_ += q_l;
344 <      sumQ2_ += q_l * q_l;
345 <    } else {
346 <      sprintf( painCave.errMsg,
347 <               "q_l value outside reasonable range\n");
348 <      painCave.severity = OOPSE_ERROR;
349 <      painCave.isFatal = 1;
350 <      simError();  
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 +    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    }  
368  
369  
370 <  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
370 >  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371 >                                               std::vector<ComplexType> What) {
372 >    
373 >    std::ofstream osq((getOutputFileName() + "q").c_str());
374  
375 <    std::ofstream os(getOutputFileName().c_str());
282 <
283 <    if (os.is_open()) {
375 >    if (osq.is_open()) {
376        
377 <      os << "# Bond Order Parameters\n";
378 <      os << "# selection: (" << selectionScript_ << ")\n";
379 <      os << "# \n";
380 <      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
381 <      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
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 < Q_histogram_.size(); ++i) {
385 <        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386 <        os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
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 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
390 >        }
391 >        osq << "\n";
392        }
393  
394 <      os.close();
394 >      osq.close();
395  
396      } else {
397        sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
398 <              getOutputFileName().c_str());
398 >              (getOutputFileName() + "q").c_str());
399        painCave.isFatal = 1;
400        simError();  
401      }
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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