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Comparing trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 2925 by chuckv, Fri Jul 7 14:18:36 2006 UTC vs.
Revision 3008 by gezelter, Tue Sep 19 21:20:15 2006 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 < *
4 < * The University of Notre Dame grants you ("Licensee") a
5 < * non-exclusive, royalty free, license to use, modify and
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
19 < *    notice, this list of conditions and the following disclaimer.
20 < *
21 < * 3. Redistributions in binary form must reproduce the above copyright
22 < *    notice, this list of conditions and the following disclaimer in the
23 < *    documentation and/or other materials provided with the
24 < *    distribution.
25 < *
26 < * This software is provided "AS IS," without a warranty of any
27 < * kind. All express or implied conditions, representations and
28 < * warranties, including any implied warranty of merchantability,
29 < * fitness for a particular purpose or non-infringement, are hereby
30 < * excluded.  The University of Notre Dame and its licensors shall not
31 < * be liable for any damages suffered by licensee as a result of
32 < * using, modifying or distributing the software or its
33 < * derivatives. In no event will the University of Notre Dame or its
34 < * licensors be liable for any lost revenue, profit or data, or for
35 < * direct, indirect, special, consequential, incidental or punitive
36 < * damages, however caused and regardless of the theory of liability,
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 <
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 < #include "applications/staticProps/BondOrderParameter.hpp"
50 < #include "utils/simError.h"
51 < #include "io/DumpReader.hpp"
52 < #include "primitives/Molecule.hpp"
53 < #include "utils/NumericConstant.hpp"
54 < #include "math/RealSphericalHarmonic.hpp"
55 < namespace oopse {
56 <
57 <
58 < BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
59 < const std::string& sele2, double rCut, int lNumber)
60 <  : StaticAnalyser(info, filename),
61 <    selectionScript1_(sele1), evaluator1_(info),
62 <    seleMan1_(info){
63 <
64 <    setOutputName(getPrefix(filename) + ".obo");
65 <        
66 <    evaluator1_.loadScriptString(sele1);
67 <    evaluator2_.loadScriptString(sele2);
68 <
69 <    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 <    }
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;
83 <
84 <  int i;
85 <  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 <
92 <     sdPairs_.push_back(std::make_pair(sd1, sd2));
93 <  }
94 <
95 <    
96 <  }
97 <
98 < void BondOrderParameter::process() {
99 <  Molecule* mol;
100 <  RigidBody* rb;
101 <  SimInfo::MoleculeIterator mi;
102 <  Molecule::RigidBodyIterator rbIter;
103 <  RealType theta;
104 <  RealType phi;
105 <  RealType r;
106 <  RealType dist;
107 <  RealType* QBar_lm;
108 <  int nBonds;
109 <  RealSphericalHarmonic sphericalHarmonic;
110 <  
111 <  
112 <  DumpReader reader(info_, dumpFilename_);    
113 <  int nFrames = reader.getNFrames();
114 <
115 <   /*Set the l for the spherical harmonic, it doesn't change*/
116 <        sphericalHarmonic.setL(lNumber_);
117 <
118 <  for (int i = 0; i < nFrames; i += step_) {
119 <    reader.readFrame(i);
120 <    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
121 <        nBonds = 0;
122 <    
123 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
124 <        //change the positions of atoms which belong to the rigidbodies
125 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
126 <            rb->updateAtoms();
127 <        }
128 <        
129 <    }      
130 <
131 <      /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
132 <      for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
133 <          Vector3d vec = j->first->getPos() - j->second->getPos();
134 <          currentSnapshot_->wrapVector(vec);
135 < /* The spherical harmonics are wrt any arbitray coordiate sysetm,
136 <  * we choose standard spherical coordinates */
137 <                r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
138 <                
139 <                /* Check to see if neighbor is in bond cuttoff*/
140 <                if (r<rCut_){          
141 <            theta = atan(vec.y()/vec.x());
142 <            phi = acos(vec.z()/r);
143 <            for(int m = -lNumber_; m <= lNumber_; m++){
144 <                sphericalHarmonic.setM(m);
145 <                QBar_lm(m) += sphericalHarmonic.getValueAt(theta,phi);
146 <            }
147 <            nBonds++;
148 <                }  
149 <      }
150 <      
151 <     /*Normalize Qbar*/
152 <     for (int m = -lNumber_;m <= lNumber_; m++){
153 <      QBar_lm(m) = QBar_lm(m)/nBonds;  
154 <     }
155 <      
156 <    
157 <  }
158 <  
159 <  /*Normalize by number of frames*/
160 <    for (int m = -lNumber_;m <= lNumber_; m++){
161 <      QBar_lm(m) = QBar_lm(m)/nFrames;  
162 <     }
163 <    
164 <    
165 <    
166 <     /* Find second order invariant Q_l*/
167 <    
168 <       for (int m = -lNumber_;m <= lNumber_; m++){
169 <         QSq_l += pow(QBar_lm(m),2);    
170 <        }
171 <     Q_l = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
172 <    
173 <     /* Find Third Order Invariant W_l*/
174 <     for (int m = -lNumber_;m<= lNumber_;m++){
175 <        
176 <        
177 <     }
178 <    
179 <    
180 <  writeOrderParameter();
181 <  
182 < }
183 <
184 < void BondOrderParameter::initalizeHistogram() {
185 <    std::fill(histogram_.begin(), histogram_.end(), 0);
186 <  }
187 <
188 < void BondOrderParameter::processHistogram() {
189 <
190 <    int nPairs = getNPairs();
191 <    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
192 <    RealType pairDensity = nPairs /volume * 2.0;
193 <    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
194 <
195 <    for(int i = 0 ; i < histogram_.size(); ++i){
196 <
197 <      RealType rLower = i * deltaR_;
198 <      RealType rUpper = rLower + deltaR_;
199 <      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
200 <      RealType nIdeal = volSlice * pairConstant;
201 <
202 <      avgGofr_[i] += histogram_[i] / nIdeal;    
203 <    }
204 <
205 <  }
206 <
207 <  void BondOrderParameter::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
208 <
209 <    if (sd1 == sd2) {
210 <      return;
211 <    }
212 <    
213 <    Vector3d pos1 = sd1->getPos();
214 <    Vector3d pos2 = sd2->getPos();
215 <    Vector3d r12 = pos2 - pos1;
216 <    currentSnapshot_->wrapVector(r12);
217 <
218 <    RealType distance = r12.length();
219 <
220 <    if (distance < len_) {
221 <      int whichBin = distance / deltaR_;
222 <      histogram_[whichBin] += 2;
223 <    }
224 <  }
225 <
226 <
227 <
228 <
229 <
230 <
231 < void BondOrderParameter::writeOrderParameter() {
232 <
233 <    std::ofstream os(getOutputFileName().c_str());
234 <    os << "#radial distribution function\n";
235 <    os<< "#selection1: (" << selectionScript1_ << ")\t";
236 <    os << "selection2: (" << selectionScript2_ << ")\n";
237 <    os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";    
238 <
239 <    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
240 <        os <<  orderParams_[i].p2 << "\t"
241 <            <<  orderParams_[i].director[0] << "\t"
242 <            <<  orderParams_[i].director[1] << "\t"
243 <            <<  orderParams_[i].director[2] << "\t"
244 <            <<  orderParams_[i].angle << "\n";
245 <
246 <    }
247 <
248 < }
249 <
250 < }
251 <
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 > *
4 > * The University of Notre Dame grants you ("Licensee") a
5 > * non-exclusive, royalty free, license to use, modify and
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
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
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 >
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 > #include "applications/staticProps/BondOrderParameter.hpp"
50 > #include "utils/simError.h"
51 > #include "io/DumpReader.hpp"
52 > #include "primitives/Molecule.hpp"
53 > #include "utils/NumericConstant.hpp"
54 > #include "math/RealSphericalHarmonic.hpp"
55 > namespace oopse {
56 >
57 >
58 >  BondOrderParameter::BondOrderParameter(SimInfo* info,
59 >                                         const std::string& filename,
60 >                                         const std::string& sele,
61 >                                         double rCut, int lNumber, int nbins)
62 >    : StaticAnalyser(info, filename), selectionScript_(sele),
63 >      evaluator_(info), seleMan_(info){
64 >    
65 >    setOutputName(getPrefix(filename) + ".obo");
66 >
67 >    evaluator_.loadScriptString(sele);
68 >    if (!evaluator_.isDynamic()) {
69 >      seleMan_.setSelectionSet(evaluator_.evaluate());
70 >    }
71 >
72 >    // Set up cutoff radius and order of the Legendre Polynomial:
73 >
74 >    lNumber_ = lNumber;
75 >    rCut_ = rCut;
76 >    mSize_ = 2*lNumber_+1;    
77 >
78 >    deltaQ_ = 1.0 / nbins;
79 >    deltaW_ = 2.0 / nbins;
80 >
81 >    Q_histogram_.resize(nbins);
82 >    W_histogram_.resize(nbins);
83 >
84 >  }
85 >
86 >  void BondOrderParameter::initalizeHistogram() {
87 >    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
88 >    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
89 >  }
90 >
91 >  void BondOrderParameter::process() {
92 >    Molecule* mol;
93 >    Atom* atom;
94 >    RigidBody* rb;
95 >    SimInfo::MoleculeIterator mi;
96 >    Molecule::RigidBodyIterator rbIter;
97 >    Molecule::AtomIterator ai;
98 >    StuntDouble* sd;
99 >    RealType theta;
100 >    RealType phi;
101 >    RealType r;
102 >    RealType dist;
103 >    std::map<int, RealType> QBar_lm;
104 >    RealType QSq_l;
105 >    RealType Q_l;
106 >    int nBonds;
107 >    RealSphericalHarmonic sphericalHarmonic;
108 >    int i, j;
109 >  
110 >    // Set the l for the spherical harmonic, it doesn't change
111 >    sphericalHarmonic.setL(lNumber_);
112 >
113 >
114 >    DumpReader reader(info_, dumpFilename_);    
115 >    int nFrames = reader.getNFrames();
116 >
117 >
118 >    for (int istep = 0; istep < nFrames; istep += step_) {
119 >      reader.readFrame(istep);
120 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
121 >      
122 >      if (evaluator_.isDynamic()) {
123 >        seleMan_.setSelectionSet(evaluator_.evaluate());
124 >      }
125 >
126 >      // update the positions of atoms which belong to the rigidbodies
127 >
128 >      for (mol = info_->beginMolecule(mi); mol != NULL;
129 >           mol = info_->nextMolecule(mi)) {
130 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
131 >             rb = mol->nextRigidBody(rbIter)) {
132 >          rb->updateAtoms();
133 >        }        
134 >      }      
135 >      
136 >      // outer loop is over the selected StuntDoubles:
137 >
138 >      for (sd = seleMan_.beginSelected(i); sd != NULL;
139 >           sd = seleMan_.nextSelected(i)) {
140 >
141 >        // For this central atom, zero out nBonds and QBar_lm
142 >
143 >        nBonds = 0;
144 >      
145 >        for (int m = -lNumber_; m <= lNumber_; m++) {
146 >          QBar_lm[m] = 0.0;
147 >        }
148 >        
149 >        // inner loop is over all other atoms in the system:
150 >        
151 >        for (mol = info_->beginMolecule(mi); mol != NULL;
152 >             mol = info_->nextMolecule(mi)) {
153 >          for (atom = mol->beginAtom(ai); atom != NULL;
154 >               atom = mol->nextAtom(ai)) {
155 >
156 >
157 >            Vector3d vec = sd->getPos() - atom->getPos();      
158 >            currentSnapshot_->wrapVector(vec);
159 >            
160 >            // Calculate "bonds" and build Q_lm(r) where
161 >            //      Q_lm = Y_lm(theta(r),phi(r))                
162 >            // The spherical harmonics are wrt any arbitrary coordinate
163 >            // system, we choose standard spherical coordinates
164 >            
165 >            r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
166 >            
167 >            // Check to see if neighbor is in bond cutoff
168 >            
169 >            if (r < rCut_) {            
170 >              theta = atan2(vec.y(), vec.x());
171 >              phi = acos(vec.z()/r);
172 >              for(int m = -lNumber_; m <= lNumber_; m++){
173 >                sphericalHarmonic.setM(m);
174 >                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
175 >              }
176 >              nBonds++;
177 >            }  
178 >          }
179 >        }
180 >        
181 >        // Normalize Qbar
182 >        for (int m = -lNumber_;m <= lNumber_; m++){
183 >          QBar_lm[m] /= nBonds;
184 >        }
185 >
186 >        // Find second order invariant Q_l
187 >
188 >        QSq_l = 0.0;
189 >        for (int m = -lNumber_; m <= lNumber_; m++){
190 >          QSq_l += pow(QBar_lm[m], 2);  
191 >        }
192 >        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
193 >    
194 >        // Find Third Order Invariant W_l
195 >
196 >        // Make arrays for Wigner3jm
197 >        double* THRCOF = new double[mSize_];
198 >        // Variables for Wigner routine
199 >        double l_ = (double)lNumber_;
200 >        double m2Min, m2Max;
201 >        int error, m1, m2, m3;
202 >
203 >        RealType W_l;
204 >        RealType W_l_hat;
205 >        W_l = 0.0;
206 >        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
207 >          // Zero work array
208 >          for (int ii = 0; ii < mSize_; ii++){
209 >            THRCOF[i] = 0.0;
210 >          }
211 >          // Get Wigner coefficients
212 >          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
213 >          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
214 >            m2 = floor(m2Min) + m_index - 1;
215 >            m3 = -m1-m2;
216 >            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
217 >          }
218 >        }
219 >
220 >        W_l_hat = W_l / pow(QSq_l, 1.5);
221 >
222 >        // accumulate histogram data for Q_l and W_l_hat:
223 >
224 >        collectHistogram(Q_l, W_l_hat);
225 >                
226 >      }
227 >    }
228 >    
229 >    // Normalize by number of frames
230 >    for (int m = -lNumber_; m <= lNumber_; m++){
231 >      QBar_lm[m] /=  nFrames;  
232 >    }
233 >    
234 >    
235 >    
236 >    
237 >    
238 >    writeOrderParameter();
239 >    
240 >  }
241 >
242 >  
243 >  void BondOrderParameter::processHistogram() {
244 >    
245 >    int nPairs = getNPairs();
246 >    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
247 >    RealType pairDensity = nPairs /volume * 2.0;
248 >    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
249 >
250 >    for(int i = 0 ; i < histogram_.size(); ++i){
251 >
252 >      RealType rLower = i * deltaR_;
253 >      RealType rUpper = rLower + deltaR_;
254 >      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
255 >      RealType nIdeal = volSlice * pairConstant;
256 >
257 >      avgGofr_[i] += histogram_[i] / nIdeal;    
258 >    }
259 >
260 >  }
261 >
262 >  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
263 >
264 >    if (Q_l < MaxQ_) {
265 >      int whichBin = Q_l / deltaQ_;
266 >      Q_histogram_[whichBin] += 1;
267 >    }
268 >    if (W_l_hat < MaxW_) {
269 >      int whichBin = W_l_hat / deltaW_;
270 >      W_histogram_[whichBin] += 1;
271 >    }
272 >  }
273 >  
274 >
275 >  void BondOrderParameter::writeOrderParameter() {
276 >
277 >    std::ofstream os(getOutputFileName().c_str());
278 >    os << "#Bond Order Parameter\n";
279 >    os << "#selection: (" << selectionScript_ << ")\n";
280 >
281 >    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
282 >      os <<  orderParams_[i].p2 << "\t"
283 >         <<  orderParams_[i].director[0] << "\t"
284 >         <<  orderParams_[i].director[1] << "\t"
285 >         <<  orderParams_[i].director[2] << "\t"
286 >         <<  orderParams_[i].angle << "\n";
287 >
288 >    }
289 >  }
290 >
291 >
292 >
293 > }

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