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root/OpenMD/trunk/src/applications/staticProps/BondOrderParameter.cpp
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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1038 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
Revision 1049 by gezelter, Fri Sep 22 01:41:11 2006 UTC

# Line 45 | Line 45
45   *     Phys Rev B, 28,784,1983
46   *
47   */
48 <
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"
54 > #include "math/SphericalHarmonic.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 lNumber, 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),
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();
65 >    evaluator_.loadScriptString(sele);
66 >    if (!evaluator_.isDynamic()) {
67 >      seleMan_.setSelectionSet(evaluator_.evaluate());
68      }
69  
70 <    /* Set up cutoff radius and type of order parameter we are calcuating*/
70 >    // Set up cutoff radius and order of the Legendre Polynomial:
71 >
72      lNumber_ = lNumber;
73      rCut_ = rCut;
74 <    mSize_ = 2*lNumber_+1;
74 >    mSize_ = 2*lNumber_+1;  
75  
76 <    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 <      for (sd2 = seleMan1_.beginSelected(j),sd2
92 <             sdPairs_.push_back(std::make_pair(sd1, sd2));
93 <           }
76 >    // Q can take values from 0 to 1
77  
78 +    MinQ_ = 0.0;
79 +    MaxQ_ = 3.0;
80 +    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81 +    Q_histogram_.resize(nbins);
82  
83 <    }
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 <    void BondOrderParameter::process
87 <      () {
88 <      Molecule* mol;
89 <      RigidBody* rb;
102 <      SimInfo::MoleculeIterator mi;
103 <      Molecule::RigidBodyIterator rbIter;
104 <      RealType theta;
105 <      RealType phi;
106 <      RealType r;
107 <      RealType dist;
108 <      RealType* QBar_lm;
109 <      RealType QSq_l;
110 <      int nBonds;
111 <      int m, m_index;
112 <      RealSphericalHarmonic sphericalHarmonic;
86 >    MinW_ = -0.18;
87 >    MaxW_ = 0.18;
88 >    deltaW_ = (MaxW_ - MinW_) / nbins;
89 >    W_histogram_.resize(nbins);
90  
91 +  }
92  
93 <      DumpReader reader(info_, dumpFilename_);
94 <      int nFrames = reader.getNFrames();
93 >  BondOrderParameter::~BondOrderParameter() {
94 >    Q_histogram_.clear();
95 >    W_histogram_.clear();
96 >  }
97  
98 <      /*Set the l for the spherical harmonic, it doesn't change*/
99 <      sphericalHarmonic.setL(lNumber_);
98 >  void BondOrderParameter::initalizeHistogram() {
99 >    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
100 >    std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
101 >  }
102  
103 <      for (int i = 0; i < nFrames; i += step_) {
104 <        reader.readFrame(i);
105 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
106 <        nBonds = 0;
103 >  void BondOrderParameter::process() {
104 >    Molecule* mol;
105 >    Atom* atom;
106 >    RigidBody* rb;
107 >    int myIndex;
108 >    SimInfo::MoleculeIterator mi;
109 >    Molecule::RigidBodyIterator rbIter;
110 >    Molecule::AtomIterator ai;
111 >    StuntDouble* sd;
112 >    Vector3d vec;
113 >    RealType costheta;
114 >    RealType phi;
115 >    RealType r;
116 >    RealType dist;
117 >    std::map<int,ComplexType> q_lm;
118 >    std::map<int,ComplexType> QBar_lm;
119 >    RealType QSq_l;
120 >    RealType Q_l;
121 >    ComplexType W_l;
122 >    ComplexType W_l_hat;
123 >    int nBonds, Nbonds;
124 >    SphericalHarmonic sphericalHarmonic;
125 >    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;
132  
133 <        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
134 <          //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 <          }
133 >    // Set the l for the spherical harmonic, it doesn't change
134 >    sphericalHarmonic.setL(lNumber_);
135  
136 <        }
136 >    DumpReader reader(info_, dumpFilename_);    
137 >    int nFrames = reader.getNFrames();
138 >    frameCounter_ = 0;
139  
140 +    for (int istep = 0; istep < nFrames; istep += step_) {
141 +      reader.readFrame(istep);
142 +      frameCounter_++;
143 +      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
144 +      
145 +      if (evaluator_.isDynamic()) {
146 +        seleMan_.setSelectionSet(evaluator_.evaluate());
147 +      }
148  
149 <        /* Setup QBar */
136 <        QBar_lm = new double[mSize_];
149 >      // update the positions of atoms which belong to the rigidbodies
150  
151 <        /* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
152 <        for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
153 <          Vector3d vec = j->first->getPos() - j->second->getPos();
154 <          currentSnapshot_->wrapVector(vec);
155 <          /* The spherical harmonics are wrt any arbitray coordiate sysetm,
156 <           * we choose standard spherical coordinates */
157 <          r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
151 >      for (mol = info_->beginMolecule(mi); mol != NULL;
152 >           mol = info_->nextMolecule(mi)) {
153 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
154 >             rb = mol->nextRigidBody(rbIter)) {
155 >          rb->updateAtoms();
156 >        }        
157 >      }          
158 >            
159 >      // outer loop is over the selected StuntDoubles:
160  
161 <          /* Check to see if neighbor is in bond cuttoff*/
162 <          if (r<rCut_){
148 <            theta = atan(vec.y()/vec.x());
149 <            phi = acos(vec.z()/r);
150 <            for(int m_index = 0; m_index < mSize_; m_index++){
151 <              sphericalHarmonic.setM(m_index-lNumber_);
152 <              QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
153 <            }
154 <            nBonds++;
155 <          }
156 <        }
161 >      for (sd = seleMan_.beginSelected(i); sd != NULL;
162 >           sd = seleMan_.nextSelected(i)) {
163  
164 <        /*Normalize Qbar by number of Bonds*/
165 <        for ( int m_index = 0;m_index < mSize_; m_index++){
166 <          QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
167 <        }
164 >        myIndex = sd->getGlobalIndex();
165 >        nBonds = 0;
166 >        for (int m = -lNumber_; m <= lNumber_; m++) {
167 >          q_lm[m] = 0.0;
168 >        }
169 >        
170 >        // inner loop is over all other atoms in the system:
171 >        
172 >        for (mol = info_->beginMolecule(mi); mol != NULL;
173 >             mol = info_->nextMolecule(mi)) {
174 >          for (atom = mol->beginAtom(ai); atom != NULL;
175 >               atom = mol->nextAtom(ai)) {
176  
177 +            if (atom->getGlobalIndex() != myIndex) {
178  
179 <      }
179 >              vec = sd->getPos() - atom->getPos();      
180 >              currentSnapshot_->wrapVector(vec);
181 >              
182 >              // Calculate "bonds" and build Q_lm(r) where
183 >              //      Q_lm = Y_lm(theta(r),phi(r))                
184 >              // The spherical harmonics are wrt any arbitrary coordinate
185 >              // system, we choose standard spherical coordinates
186 >              
187 >              r = vec.length();
188 >              
189 >              // Check to see if neighbor is in bond cutoff
190 >              
191 >              if (r < rCut_) {
192 >                costheta = vec.z() / r;
193 >                phi = atan2(vec.y(), vec.x());
194 >                
195 >                for(int m = -lNumber_; m <= lNumber_; m++){
196 >                  sphericalHarmonic.setM(m);
197 >                  q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
198 >                }
199 >                nBonds++;
200 >              }  
201 >            }
202 >          }
203 >        }
204 >        RealType ql = 0.0;
205 >        for(int m=-lNumber_; m<=lNumber_; m++) {          
206 >          ql += norm(QBar_lm[m]);
207 >        }        
208 >        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
209 >        collectHistogram(sqrt(ql)/(RealType)nBonds);
210  
211 <      /*Normalize by number of frames*/
212 <      for ( int m_index = 0;m_index < mSize_; m_index++){
213 <        QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
211 >        Nbonds += nBonds;
212 >        for (int m=-lNumber_; m<=lNumber_; m++) {
213 >          QBar_lm[m] += q_lm[m];
214 >        }
215        }
216 +    }
217  
218 <
219 <
220 <      /* Find second order invariant Q_l*/
221 <
222 <      for (int m_index = 0 ;m_index <= sizeM_; m++){
223 <        QSq_l += pow(QBar_lm(m),2);
218 >    // Normalize Qbar2
219 >    for (int m = -lNumber_;m <= lNumber_; m++){
220 >      QBar_lm[m] /= Nbonds;
221 >    }
222 >    
223 >    // Find second order invariant Q_l
224 >    
225 >    QSq_l = 0.0;
226 >    for (int m = -lNumber_; m <= lNumber_; m++){
227 >      QSq_l += norm(QBar_lm[m]);
228 >    }
229 >    
230 >    std::cout << "qsl = " << QSq_l << "\n";
231 >    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
232 >    
233 >    // Find Third Order Invariant W_l
234 >    
235 >    W_l = 0.0;
236 >    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
237 >      // Zero work array
238 >      for (int ii = 0; ii < mSize_; ii++){
239 >        THRCOF[ii] = 0.0;
240        }
241 <      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
242 <
243 <      /* Find Third Order Invariant W_l*/
244 <
245 <      /* Make arrays for Wigner3jm */
246 <      double* THRCOF = new double[mSize_];
247 <      /* Variables for Wigner routine */
248 <      double l_ = (double)lNumber_;
249 <      double m2Min;
250 <      double m2Max;
251 <      int error;
189 <      int m1;
190 <      int m2;
191 <      int m3;
192 <
193 <      for (int m1 = -lNumber_;m <= lNumber_;m1++){
194 <        /* Zero work array */
195 <        for (i=0; i<mSize_;i++){
196 <          THRCOF[i] = 0.0;      
197 <        }
198 <        /* Get wigner coefficients */
199 <        Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
200 <        for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
201 <          m2 = floor(m2Min) + m_index - 1;
202 <          m3 = -m1-m2;
203 <          W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
204 <        }
241 >      // Get Wigner coefficients
242 >      m1Pass = (double)m1;
243 >      
244 >      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        }
253 +    }
254 +    
255 +    W_l_hat = W_l / pow(QSq_l, 1.5);              
256 +    
257 +    writeOrderParameter(Q_l, real(W_l_hat));    
258 +  }
259  
260 +  void BondOrderParameter::collectHistogram(RealType q_l) {
261  
262 <      writeOrderParameter();
263 <
262 >    if (q_l >= MinQ_ && q_l < MaxQ_) {
263 >      int qbin = (q_l - MinQ_) / deltaQ_;
264 >      Q_histogram_[qbin] += 1;
265 >      Qcount_++;
266 >      sumQ_ += q_l;
267 >      sumQ2_ += q_l * q_l;
268 >    } else {
269 >      sprintf( painCave.errMsg,
270 >               "q_l value outside reasonable range\n");
271 >      painCave.severity = OOPSE_ERROR;
272 >      painCave.isFatal = 1;
273 >      simError();  
274      }
275  
276 +  }  
277  
213 –    void BondOrderParameter::writeOrderParameter() {
278  
279 <      std::ofstream os(getOutputFileName().c_str());
216 <      os << "#radial distribution function\n";
217 <      os<< "#selection1: (" << selectionScript1_ << ")\t";
218 <      os << "selection2: (" << selectionScript2_ << ")\n";
219 <      os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
279 >  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
280  
281 <      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";
281 >    std::ofstream os(getOutputFileName().c_str());
282  
283 +    if (os.is_open()) {
284 +      
285 +      os << "# Bond Order Parameters\n";
286 +      os << "# selection: (" << selectionScript_ << ")\n";
287 +      os << "# \n";
288 +      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
289 +      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
290 +      // Normalize by number of frames and write it out:
291 +      for (int i = 0; i < Q_histogram_.size(); ++i) {
292 +        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
293 +        os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
294        }
295  
296 <    }
296 >      os.close();
297  
298 +    } else {
299 +      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
300 +              getOutputFileName().c_str());
301 +      painCave.isFatal = 1;
302 +      simError();  
303 +    }
304    }
305 <
305 > }

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