--- trunk/src/applications/staticProps/BondOrderParameter.cpp	2006/09/18 21:31:23	1038
+++ trunk/src/applications/staticProps/BondOrderParameter.cpp	2006/09/21 21:47:17	1047
@@ -45,189 +45,204 @@
  *     Phys Rev B, 28,784,1983
  * 
  */
-
+ 
 #include "applications/staticProps/BondOrderParameter.hpp"
 #include "utils/simError.h"
 #include "io/DumpReader.hpp"
 #include "primitives/Molecule.hpp"
 #include "utils/NumericConstant.hpp"
-#include "math/RealSphericalHarmonic.hpp"
+#include "math/SphericalHarmonic.hpp"
+
 namespace oopse {
 
+  BondOrderParameter::BondOrderParameter(SimInfo* info, 
+                                         const std::string& filename, 
+                                         const std::string& sele,
+                                         double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
+    
+    setOutputName(getPrefix(filename) + ".bo");
 
-  BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
-					 const std::string& sele2, double rCut, int lNumber)
-    : StaticAnalyser(info, filename),
-      selectionScript1_(sele1), evaluator1_(info),
-      seleMan1_(info){
-
-    setOutputName(getPrefix(filename) + ".obo");
-
-    evaluator1_.loadScriptString(sele1);
-    evaluator2_.loadScriptString(sele2);
-
-    if (!evaluator1_.isDynamic()) {
-      seleMan1_.setSelectionSet(evaluator1_.evaluate());
-    }else {
-      sprintf( painCave.errMsg,
-	       "--sele1 must be static selection\n");
-      painCave.severity = OOPSE_ERROR;
-      painCave.isFatal = 1;
-      simError();
+    evaluator_.loadScriptString(sele);
+    if (!evaluator_.isDynamic()) {
+      seleMan_.setSelectionSet(evaluator_.evaluate());
     }
 
-    /* Set up cutoff radius and type of order parameter we are calcuating*/
+    // Set up cutoff radius and order of the Legendre Polynomial:
+
     lNumber_ = lNumber;
     rCut_ = rCut;
-    mSize_ = 2*lNumber_+1;
+    mSize_ = 2*lNumber_+1;    
+  }
 
-    int i;
-    int j;
-    StuntDouble* sd1;
-    StuntDouble* sd2;
-    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
-	 sd1 != NULL && sd2 != NULL;
-	 sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
-      for (sd2 = seleMan1_.beginSelected(j),sd2
-	     sdPairs_.push_back(std::make_pair(sd1, sd2));
-	   }
+  BondOrderParameter::~BondOrderParameter() {
+  }
 
+  void BondOrderParameter::process() {
+    Molecule* mol;
+    Atom* atom;
+    RigidBody* rb;
+    int myIndex;
+    SimInfo::MoleculeIterator mi;
+    Molecule::RigidBodyIterator rbIter;
+    Molecule::AtomIterator ai;
+    StuntDouble* sd;
+    Vector3d vec;
+    RealType costheta;
+    RealType phi;
+    RealType r;
+    RealType dist;
+    std::map<int,ComplexType> QBar_lm;
+    RealType QSq_l;
+    RealType Q_l;
+    ComplexType W_l;
+    ComplexType W_l_hat;
+    int nBonds;
+    SphericalHarmonic sphericalHarmonic;
+    int i, j;
+    // Make arrays for Wigner3jm
+    double* THRCOF = new double[mSize_];
+    // Variables for Wigner routine
+    double l_ = (double)lNumber_;
+    double m1Pass, m2Min, m2Max;
+    int error, m1, m2, m3;
 
-    }
+    // Set the l for the spherical harmonic, it doesn't change
+    sphericalHarmonic.setL(lNumber_);
 
-    void BondOrderParameter::process
-      () {
-      Molecule* mol;
-      RigidBody* rb;
-      SimInfo::MoleculeIterator mi;
-      Molecule::RigidBodyIterator rbIter;
-      RealType theta;
-      RealType phi;
-      RealType r;
-      RealType dist;
-      RealType* QBar_lm;
-      RealType QSq_l;
-      int nBonds;
-      int m, m_index;
-      RealSphericalHarmonic sphericalHarmonic;
+    DumpReader reader(info_, dumpFilename_);    
+    int nFrames = reader.getNFrames();
+    frameCounter_ = 0;
 
+    for (int istep = 0; istep < nFrames; istep += step_) {
+      reader.readFrame(istep);
+      frameCounter_++;
+      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
+      
+      if (evaluator_.isDynamic()) {
+        seleMan_.setSelectionSet(evaluator_.evaluate());
+      }
 
-      DumpReader reader(info_, dumpFilename_);
-      int nFrames = reader.getNFrames();
+      // update the positions of atoms which belong to the rigidbodies
 
-      /*Set the l for the spherical harmonic, it doesn't change*/
-      sphericalHarmonic.setL(lNumber_);
-
-      for (int i = 0; i < nFrames; i += step_) {
-	reader.readFrame(i);
-	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
-	nBonds = 0;
-
-	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
-	  //change the positions of atoms which belong to the rigidbodies
-	  for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
-	    rb->updateAtoms();
-	  }
-
-	}
-
-
-	/* Setup QBar */
-	QBar_lm = new double[mSize_];
-
-	/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
-	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
-	  Vector3d vec = j->first->getPos() - j->second->getPos();
-	  currentSnapshot_->wrapVector(vec);
-	  /* The spherical harmonics are wrt any arbitray coordiate sysetm,
-	   * we choose standard spherical coordinates */
-	  r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
-
-	  /* Check to see if neighbor is in bond cuttoff*/
-	  if (r<rCut_){
-	    theta = atan(vec.y()/vec.x());
-	    phi = acos(vec.z()/r);
-	    for(int m_index = 0; m_index < mSize_; m_index++){
-	      sphericalHarmonic.setM(m_index-lNumber_);
-	      QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
-	    }
-	    nBonds++;
-	  }
-	}
-
-	/*Normalize Qbar by number of Bonds*/
-	for ( int m_index = 0;m_index < mSize_; m_index++){
-	  QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
-	}
-
-
+      for (mol = info_->beginMolecule(mi); mol != NULL; 
+           mol = info_->nextMolecule(mi)) {
+        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+             rb = mol->nextRigidBody(rbIter)) {
+          rb->updateAtoms();
+        }        
+      }      
+      
+      nBonds = 0;
+      
+      for (int m = -lNumber_; m <= lNumber_; m++) {
+        QBar_lm[m] = 0.0;
       }
+      
+      // outer loop is over the selected StuntDoubles:
 
-      /*Normalize by number of frames*/
-      for ( int m_index = 0;m_index < mSize_; m_index++){
-	QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
-      }
+      for (sd = seleMan_.beginSelected(i); sd != NULL; 
+           sd = seleMan_.nextSelected(i)) {
 
+        myIndex = sd->getGlobalIndex();
+        
+        // inner loop is over all other atoms in the system:
+        
+        for (mol = info_->beginMolecule(mi); mol != NULL; 
+             mol = info_->nextMolecule(mi)) {
+          for (atom = mol->beginAtom(ai); atom != NULL; 
+               atom = mol->nextAtom(ai)) {
 
+            if (atom->getGlobalIndex() != myIndex) {
 
-      /* Find second order invariant Q_l*/
+              vec = sd->getPos() - atom->getPos();       
+              currentSnapshot_->wrapVector(vec);
+              
+              // Calculate "bonds" and build Q_lm(r) where 
+              //      Q_lm = Y_lm(theta(r),phi(r))                
+              // The spherical harmonics are wrt any arbitrary coordinate
+              // system, we choose standard spherical coordinates 
+              
+              r = vec.length();
+              
+              // Check to see if neighbor is in bond cutoff 
+              
+              if (r < rCut_) { 
+                costheta = vec.z() / r; 
+                phi = atan2(vec.y(), vec.x());
+                
+                for(int m = -lNumber_; m <= lNumber_; m++){
+                  sphericalHarmonic.setM(m);
+                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
+                }
+                nBonds++;
+              }  
+            }
+          }
+        }
+      }      
+    }
 
-      for (int m_index = 0 ;m_index <= sizeM_; m++){
-	QSq_l += pow(QBar_lm(m),2);
+    // Normalize Qbar2
+    for (int m = -lNumber_;m <= lNumber_; m++){
+      QBar_lm[m] /= nBonds;
+    }
+    
+    // Find second order invariant Q_l
+    
+    QSq_l = 0.0;
+    for (int m = -lNumber_; m <= lNumber_; m++){
+      QSq_l += norm(QBar_lm[m]);
+    }
+    
+    std::cout << "qsl = " << QSq_l << "\n";
+    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
+    
+    // Find Third Order Invariant W_l
+    
+    W_l = 0.0;
+    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
+      // Zero work array
+      for (int ii = 0; ii < mSize_; ii++){
+        THRCOF[ii] = 0.0;
       }
-      Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
-
-      /* Find Third Order Invariant W_l*/
-
-      /* Make arrays for Wigner3jm */
-      double* THRCOF = new double[mSize_];
-      /* Variables for Wigner routine */
-      double l_ = (double)lNumber_;
-      double m2Min;
-      double m2Max;
-      int error;
-      int m1;
-      int m2;
-      int m3;
-
-      for (int m1 = -lNumber_;m <= lNumber_;m1++){
-	/* Zero work array */
-	for (i=0; i<mSize_;i++){
-	  THRCOF[i] = 0.0;      
-	}
-	/* Get wigner coefficients */
-	Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
-	for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
-	  m2 = floor(m2Min) + m_index - 1;
-	  m3 = -m1-m2;
-	  W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
-	}
+      // Get Wigner coefficients
+      m1Pass = (double)m1;
+      
+      Wigner3jm(&l_, &l_, &l_, 
+                &m1Pass, &m2Min, &m2Max, 
+                THRCOF, &mSize_, &error);
+      
+      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
+        m2 = (int)floor(m2Min) + mmm;
+        m3 = -m1-m2;
+        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
       }
-
-
-      writeOrderParameter();
-
     }
+    
+    W_l_hat = W_l / pow(QSq_l, 1.5);               
+    
+    writeOrderParameter(Q_l, real(W_l_hat));    
+  }
 
 
-    void BondOrderParameter::writeOrderParameter() {
+  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
 
-      std::ofstream os(getOutputFileName().c_str());
-      os << "#radial distribution function\n";
-      os<< "#selection1: (" << selectionScript1_ << ")\t";
-      os << "selection2: (" << selectionScript2_ << ")\n";
-      os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
+    std::ofstream os(getOutputFileName().c_str());
 
-      for (std::size_t i = 0; i < orderParams_.size(); ++i) {
-	os <<  orderParams_[i].p2 << "\t"
-	   <<  orderParams_[i].director[0] << "\t"
-	   <<  orderParams_[i].director[1] << "\t"
-	   <<  orderParams_[i].director[2] << "\t"
-	   <<  orderParams_[i].angle << "\n";
+    if (os.is_open()) {
+      
+      os << "# Bond Order Parameters\n";
+      os << "# selection: (" << selectionScript_ << ")\n";
+      os << "# \n";
+      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
+      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
+      os.close();
 
-      }
-
+    } else {
+      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
+              getOutputFileName().c_str());
+      painCave.isFatal = 1;
+      simError();  
     }
-
   }
-
+}