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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1052 by gezelter, Tue Sep 26 01:30:32 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"
# Line 52 | Line 50
50   #include "primitives/Molecule.hpp"
51   #include "utils/NumericConstant.hpp"
52  
53 < namespace oopse {
53 > namespace OpenMD {
54  
55    BondOrderParameter::BondOrderParameter(SimInfo* info,
56                                           const std::string& filename,
# Line 82 | Line 80 | namespace oopse {
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_ = -0.25;
84 <    MaxW_ = 0.25;
83 >    MinW_ = -1.1;
84 >    MaxW_ = 1.1;
85      deltaW_ = (MaxW_ - MinW_) / nbins;
88 –  }
86  
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      for (int bin = 0; bin < nBins_; bin++) {
138        for (int l = 0; l <= lMax_; l++) {
# Line 128 | Line 169 | namespace oopse {
169      int nBonds, Nbonds;
170      SphericalHarmonic sphericalHarmonic;
171      int i, j;
131 –    // Make arrays for Wigner3jm
132 –    double* THRCOF = new double[2*lMax_+1];
133 –    // Variables for Wigner routine
134 –    double lPass, m1Pass, m2Min, m2Max;
135 –    int error, m1, m2, m3, mSize;
136 –    mSize = 2*lMax_+1;
172  
173      DumpReader reader(info_, dumpFilename_);    
174      int nFrames = reader.getNFrames();
# Line 148 | Line 183 | namespace oopse {
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);
# Line 192 | 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 221 | Line 259 | namespace oopse {
259          }
260          
261          
224 –        for (int l = 0; l <= lMax_; l++) {        
225 –          q_l[l] = 0.0;
226 –          for(int m = -l; m <= l; m++) {
227 –            q_l[l] += norm(q[std::make_pair(l,m)]);
228 –          }    
229 –          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
230 –          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231 –        }
232 –
233 –        // Find second order invariant Q_l
234 –        
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 /
241 <                        (RealType)(2*l + 1))/(RealType)nBonds;
268 >          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
269          }
270 <
270 >        
271          // Find Third Order Invariant W_l
272      
273          for (int l = 0; l <= lMax_; l++) {
274            w[l] = 0.0;
248 –          lPass = (double)l;
275            for (int m1 = -l; m1 <= l; m1++) {
276 <            // Zero work array
277 <            for (int ii = 0; ii < 2*l + 1; ii++){
278 <              THRCOF[ii] = 0.0;
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              }
254 –            // Get Wigner coefficients
255 –            m1Pass = (double)m1;
256 –            
257 –            Wigner3jm(&lPass, &lPass, &lPass,
258 –                      &m1Pass, &m2Min, &m2Max,
259 –                      THRCOF, &mSize, &error);
260 –            
261 –            for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
262 –              m2 = (int)floor(m2Min) + mmm;
263 –              m3 = -m1-m2;
264 –              w[l] += THRCOF[mmm] *
265 –                q[std::make_pair(l,m1)] *
266 –                q[std::make_pair(l,m2)] *
267 –                q[std::make_pair(l,m3)];
268 –            }
283            }
284            
285            w_hat[l] = w[l] / pow(q2[l], 1.5);
# Line 276 | Line 290 | namespace oopse {
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)] += q[std::make_pair(l,m)];
293 >            QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
294            }
295          }
296        }
# Line 303 | Line 317 | namespace oopse {
317      
318      for (int l = 0; l <= lMax_; l++) {
319        W[l] = 0.0;
306 –      lPass = (double)l;
320        for (int m1 = -l; m1 <= l; m1++) {
321 <        // Zero work array
322 <        for (int ii = 0; ii < 2*l + 1; ii++){
323 <          THRCOF[ii] = 0.0;
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          }
312 –        // Get Wigner coefficients
313 –        m1Pass = (double)m1;
314 –        
315 –        Wigner3jm(&lPass, &lPass, &lPass,
316 –                  &m1Pass, &m2Min, &m2Max,
317 –                  THRCOF, &mSize, &error);
318 –        
319 –        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
320 –          m2 = (int)floor(m2Min) + mmm;
321 –          m3 = -m1-m2;
322 –          W[l] += THRCOF[mmm] *
323 –            QBar[std::make_pair(l,m1)] *
324 –            QBar[std::make_pair(l,m2)] *
325 –            QBar[std::make_pair(l,m3)];
326 –        }
328        }
329        
330        W_hat[l] = W[l] / pow(Q2[l], 1.5);
# Line 343 | Line 344 | namespace oopse {
344        } else {
345          sprintf( painCave.errMsg,
346                   "q_l value outside reasonable range\n");
347 <        painCave.severity = OOPSE_ERROR;
347 >        painCave.severity = OPENMD_ERROR;
348          painCave.isFatal = 1;
349          simError();  
350        }
# Line 356 | Line 357 | namespace oopse {
357          Wcount_[l]++;      
358        } else {
359          sprintf( painCave.errMsg,
360 <                 "Re[w_hat] value outside reasonable range\n");
361 <        painCave.severity = OOPSE_ERROR;
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        }
# Line 384 | Line 385 | namespace oopse {
385          RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;              
386          osq << Qval;
387          for (int l = 0; l <= lMax_; l++) {
388 <          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
388 >
389 >          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
390          }
391          osq << "\n";
392        }
# Line 405 | Line 407 | namespace oopse {
407        osw << "# selection: (" << selectionScript_ << ")\n";
408        osw << "# \n";
409        for (int l = 0; l <= lMax_; l++) {
410 <        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
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 <          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
417 >
418 >          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
419          }
420          osw << "\n";
421        }

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