applications/staticProps/BondOrderParameter.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */


/* Creates orientational bond order parameters as outlined by
 *     Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
 *     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"

namespace oopse {

  BondOrderParameter::BondOrderParameter(SimInfo* info, 
                                         const std::string& filename, 
                                         const std::string& sele,
                                         double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
    
    setOutputName(getPrefix(filename) + ".bo");

    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }

    // Set up cutoff radius and order of the Legendre Polynomial:

    rCut_ = rCut;
    nBins_ = nbins;
    Qcount_.resize(lMax_+1);
    Wcount_.resize(lMax_+1);

    // Q can take values from 0 to 1

    MinQ_ = 0.0;
    MaxQ_ = 1.1;
    deltaQ_ = (MaxQ_ - MinQ_) / nbins;

    // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
    // use values for MinW_ and MaxW_ that are slightly larger than this:

    MinW_ = -0.25;
    MaxW_ = 0.25;
    deltaW_ = (MaxW_ - MinW_) / nbins;
  }

  BondOrderParameter::~BondOrderParameter() {
    Q_histogram_.clear();
    W_histogram_.clear();
  }

  void BondOrderParameter::initalizeHistogram() {
    for (int bin = 0; bin < nBins_; bin++) {
      for (int l = 0; l <= lMax_; l++) {
        Q_histogram_[std::make_pair(bin,l)] = 0;
        W_histogram_[std::make_pair(bin,l)] = 0;
      }
    }
  }

  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<std::pair<int,int>,ComplexType> q;
    std::vector<RealType> q_l;
    std::vector<RealType> q2;
    std::vector<ComplexType> w;
    std::vector<ComplexType> w_hat;
    std::map<std::pair<int,int>,ComplexType> QBar;
    std::vector<RealType> Q2;
    std::vector<RealType> Q;
    std::vector<ComplexType> W;
    std::vector<ComplexType> W_hat;
    int nBonds, Nbonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;
    // Make arrays for Wigner3jm
    double* THRCOF = new double[2*lMax_+1];
    // Variables for Wigner routine
    double lPass, m1Pass, m2Min, m2Max;
    int error, m1, m2, m3, mSize;
    mSize = 2*lMax_+1;

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    frameCounter_ = 0;

    q_l.resize(lMax_+1);
    q2.resize(lMax_+1);
    w.resize(lMax_+1);
    w_hat.resize(lMax_+1);

    Q2.resize(lMax_+1);
    Q.resize(lMax_+1);
    W.resize(lMax_+1);
    W_hat.resize(lMax_+1);

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }

      // update the positions of atoms which belong to the rigidbodies

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }        
      }           
            
      // outer loop is over the selected StuntDoubles:

      for (sd = seleMan_.beginSelected(i); sd != NULL; 
           sd = seleMan_.nextSelected(i)) {

        myIndex = sd->getGlobalIndex();
        nBonds = 0;
        
        for (int l = 0; l <= lMax_; l++) {
          for (int m = -l; m <= l; m++) {
            q[std::make_pair(l,m)] = 0.0;
          }
        }
        
        // 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) {

              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 l = 0; l <= lMax_; l++) {
                  sphericalHarmonic.setL(l);
                  for(int m = -l; m <= l; m++){
                    sphericalHarmonic.setM(m);
                    q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
                  }
                }
                nBonds++;
              }  
            }
          }
        }
        
        
        for (int l = 0; l <= lMax_; l++) {         
          q_l[l] = 0.0;
          for(int m = -l; m <= l; m++) { 
            q_l[l] += norm(q[std::make_pair(l,m)]);
          }     
          q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
          q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
        }

        // Find second order invariant Q_l
        
        for (int l = 0; l <= lMax_; l++) {
          q2[l] = 0.0;
          for (int m = -l; m <= l; m++){
            q2[l] += norm(q[std::make_pair(l,m)]);
          }
          q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / 
                        (RealType)(2*l + 1))/(RealType)nBonds;
        }

        // Find Third Order Invariant W_l
    
        for (int l = 0; l <= lMax_; l++) {
          w[l] = 0.0;
          lPass = (double)l;
          for (int m1 = -l; m1 <= l; m1++) {
            // Zero work array
            for (int ii = 0; ii < 2*l + 1; ii++){
              THRCOF[ii] = 0.0;
            }
            // Get Wigner coefficients
            m1Pass = (double)m1;
            
            Wigner3jm(&lPass, &lPass, &lPass, 
                      &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] * 
                q[std::make_pair(l,m1)] * 
                q[std::make_pair(l,m2)] * 
                q[std::make_pair(l,m3)];
            }
          }
          
          w_hat[l] = w[l] / pow(q2[l], 1.5);
        }

        collectHistogram(q_l, w_hat);
        
        Nbonds += nBonds;
        for (int l = 0; l <= lMax_;  l++) {
          for (int m = -l; m <= l; m++) {
            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
          }
        }
      }
    }
      
    // Normalize Qbar2
    for (int l = 0; l <= lMax_; l++) {
      for (int m = -l; m <= l; m++){
        QBar[std::make_pair(l,m)] /= Nbonds;
      }
    }
    
    // Find second order invariant Q_l
    
    for (int l = 0; l <= lMax_; l++) {
      Q2[l] = 0.0;
      for (int m = -l; m <= l; m++){
        Q2[l] += norm(QBar[std::make_pair(l,m)]);
      }
      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
    }
    
    // Find Third Order Invariant W_l
    
    for (int l = 0; l <= lMax_; l++) {
      W[l] = 0.0;
      lPass = (double)l;
      for (int m1 = -l; m1 <= l; m1++) {
        // Zero work array
        for (int ii = 0; ii < 2*l + 1; ii++){
          THRCOF[ii] = 0.0;
        }
        // Get Wigner coefficients
        m1Pass = (double)m1;
        
        Wigner3jm(&lPass, &lPass, &lPass, 
                  &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[std::make_pair(l,m1)] * 
            QBar[std::make_pair(l,m2)] * 
            QBar[std::make_pair(l,m3)];
        }
      }
      
      W_hat[l] = W[l] / pow(Q2[l], 1.5);
    }
    
    writeOrderParameter(Q, W_hat);    
  }

  void BondOrderParameter::collectHistogram(std::vector<RealType> q, 
                                            std::vector<ComplexType> what) {

    for (int l = 0; l <= lMax_; l++) {
      if (q[l] >= MinQ_ && q[l] < MaxQ_) {
        int qbin = (q[l] - MinQ_) / deltaQ_;
        Q_histogram_[std::make_pair(qbin,l)] += 1;
        Qcount_[l]++;      
      } else {
        sprintf( painCave.errMsg,
                 "q_l value outside reasonable range\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
      }
    }

    for (int l = 0; l <= lMax_; l++) {
      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
        int wbin = (real(what[l]) - MinW_) / deltaW_;
        W_histogram_[std::make_pair(wbin,l)] += 1;
        Wcount_[l]++;      
      } else {
        sprintf( painCave.errMsg,
                 "Re[w_hat] value outside reasonable range\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
      }
    }

  }  


  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, 
                                               std::vector<ComplexType> What) {
    
    std::ofstream osq((getOutputFileName() + "q").c_str());

    if (osq.is_open()) {
      
      osq << "# Bond Order Parameters\n";
      osq << "# selection: (" << selectionScript_ << ")\n";
      osq << "# \n";
      for (int l = 0; l <= lMax_; l++) {
        osq << "# <Q_" << l << ">: " << Q[l] << "\n";
      }
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;               
        osq << Qval;
        for (int l = 0; l <= lMax_; l++) {
          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
        }
        osq << "\n";
      }

      osq.close();

    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "q").c_str());
      painCave.isFatal = 1;
      simError();  
    }

    std::ofstream osw((getOutputFileName() + "w").c_str());

    if (osw.is_open()) {
      osw << "# Bond Order Parameters\n";
      osw << "# selection: (" << selectionScript_ << ")\n";
      osw << "# \n";
      for (int l = 0; l <= lMax_; l++) {
        osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
      }
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Wval = MinW_ + (i + 0.5) * deltaW_;               
        osw << Wval;
        for (int l = 0; l <= lMax_; l++) {
          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
        }
        osw << "\n";
      }

      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
       
  }
}
Revision:	3022
Committed:	Tue Sep 26 01:30:32 2006 UTC (17 years, 9 months ago) by gezelter
File size:	13820 byte(s)
Log Message:	Mostly done with BondOrderParameter. Only a few performance tweaks remain
#	User	Rev	Content
1	chuckv	3005	/*
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	gezelter	3007
49	chuckv	3005	#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	gezelter	3009
55	chuckv	3005	namespace oopse {
56
57	gezelter	3007	BondOrderParameter::BondOrderParameter(SimInfo* info,
58			const std::string& filename,
59			const std::string& sele,
60	gezelter	3022	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61	gezelter	3007
62	gezelter	3009	setOutputName(getPrefix(filename) + ".bo");
63	chuckv	3005
64	gezelter	3007	evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67	chuckv	3005	}
68
69	gezelter	3007	// Set up cutoff radius and order of the Legendre Polynomial:
70
71	chuckv	3005	rCut_ = rCut;
72	gezelter	3021	nBins_ = nbins;
73			Qcount_.resize(lMax_+1);
74			Wcount_.resize(lMax_+1);
75	gezelter	3017
76			// Q can take values from 0 to 1
77
78			MinQ_ = 0.0;
79	gezelter	3021	MaxQ_ = 1.1;
80	gezelter	3017	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81
82			// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
83			// use values for MinW_ and MaxW_ that are slightly larger than this:
84
85	gezelter	3022	MinW_ = -0.25;
86			MaxW_ = 0.25;
87	gezelter	3017	deltaW_ = (MaxW_ - MinW_) / nbins;
88	gezelter	3007	}
89	chuckv	3005
90	gezelter	3009	BondOrderParameter::~BondOrderParameter() {
91	gezelter	3017	Q_histogram_.clear();
92			W_histogram_.clear();
93	gezelter	3009	}
94
95	gezelter	3017	void BondOrderParameter::initalizeHistogram() {
96	gezelter	3021	for (int bin = 0; bin < nBins_; bin++) {
97			for (int l = 0; l <= lMax_; l++) {
98			Q_histogram_[std::make_pair(bin,l)] = 0;
99			W_histogram_[std::make_pair(bin,l)] = 0;
100			}
101			}
102	gezelter	3017	}
103
104	gezelter	3007	void BondOrderParameter::process() {
105			Molecule* mol;
106			Atom* atom;
107			RigidBody* rb;
108	gezelter	3011	int myIndex;
109	gezelter	3007	SimInfo::MoleculeIterator mi;
110			Molecule::RigidBodyIterator rbIter;
111			Molecule::AtomIterator ai;
112			StuntDouble* sd;
113	gezelter	3011	Vector3d vec;
114	gezelter	3010	RealType costheta;
115	gezelter	3007	RealType phi;
116			RealType r;
117			RealType dist;
118	gezelter	3021	std::map<std::pair<int,int>,ComplexType> q;
119			std::vector<RealType> q_l;
120	gezelter	3022	std::vector<RealType> q2;
121			std::vector<ComplexType> w;
122			std::vector<ComplexType> w_hat;
123	gezelter	3021	std::map<std::pair<int,int>,ComplexType> QBar;
124			std::vector<RealType> Q2;
125			std::vector<RealType> Q;
126			std::vector<ComplexType> W;
127			std::vector<ComplexType> W_hat;
128	gezelter	3017	int nBonds, Nbonds;
129	gezelter	3010	SphericalHarmonic sphericalHarmonic;
130	gezelter	3007	int i, j;
131	gezelter	3011	// Make arrays for Wigner3jm
132	gezelter	3021	double* THRCOF = new double[2*lMax_+1];
133	gezelter	3011	// Variables for Wigner routine
134	gezelter	3021	double lPass, m1Pass, m2Min, m2Max;
135			int error, m1, m2, m3, mSize;
136			mSize = 2*lMax_+1;
137	gezelter	3011
138	gezelter	3007	DumpReader reader(info_, dumpFilename_);
139			int nFrames = reader.getNFrames();
140	gezelter	3009	frameCounter_ = 0;
141	chuckv	3005
142	gezelter	3021	q_l.resize(lMax_+1);
143	gezelter	3022	q2.resize(lMax_+1);
144			w.resize(lMax_+1);
145			w_hat.resize(lMax_+1);
146
147	gezelter	3021	Q2.resize(lMax_+1);
148			Q.resize(lMax_+1);
149			W.resize(lMax_+1);
150			W_hat.resize(lMax_+1);
151
152	gezelter	3007	for (int istep = 0; istep < nFrames; istep += step_) {
153			reader.readFrame(istep);
154	gezelter	3009	frameCounter_++;
155	gezelter	3007	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
156
157			if (evaluator_.isDynamic()) {
158			seleMan_.setSelectionSet(evaluator_.evaluate());
159			}
160	chuckv	3005
161	gezelter	3007	// update the positions of atoms which belong to the rigidbodies
162	chuckv	3005
163	gezelter	3007	for (mol = info_->beginMolecule(mi); mol != NULL;
164			mol = info_->nextMolecule(mi)) {
165			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
166			rb = mol->nextRigidBody(rbIter)) {
167			rb->updateAtoms();
168			}
169	gezelter	3017	}
170
171	gezelter	3007	// outer loop is over the selected StuntDoubles:
172	chuckv	3005
173	gezelter	3007	for (sd = seleMan_.beginSelected(i); sd != NULL;
174			sd = seleMan_.nextSelected(i)) {
175	chuckv	3005
176	gezelter	3011	myIndex = sd->getGlobalIndex();
177	gezelter	3017	nBonds = 0;
178	gezelter	3021
179			for (int l = 0; l <= lMax_; l++) {
180			for (int m = -l; m <= l; m++) {
181			q[std::make_pair(l,m)] = 0.0;
182			}
183	gezelter	3017	}
184	gezelter	3007
185			// inner loop is over all other atoms in the system:
186
187			for (mol = info_->beginMolecule(mi); mol != NULL;
188			mol = info_->nextMolecule(mi)) {
189			for (atom = mol->beginAtom(ai); atom != NULL;
190			atom = mol->nextAtom(ai)) {
191	chuckv	3005
192	gezelter	3011	if (atom->getGlobalIndex() != myIndex) {
193	chuckv	3005
194	gezelter	3011	vec = sd->getPos() - atom->getPos();
195			currentSnapshot_->wrapVector(vec);
196	gezelter	3010
197	gezelter	3011	// Calculate "bonds" and build Q_lm(r) where
198			// Q_lm = Y_lm(theta(r),phi(r))
199			// The spherical harmonics are wrt any arbitrary coordinate
200			// system, we choose standard spherical coordinates
201
202			r = vec.length();
203
204			// Check to see if neighbor is in bond cutoff
205
206			if (r < rCut_) {
207			costheta = vec.z() / r;
208			phi = atan2(vec.y(), vec.x());
209	gezelter	3021
210			for (int l = 0; l <= lMax_; l++) {
211			sphericalHarmonic.setL(l);
212			for(int m = -l; m <= l; m++){
213			sphericalHarmonic.setM(m);
214			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
215			}
216	gezelter	3011	}
217			nBonds++;
218			}
219			}
220	gezelter	3007	}
221			}
222	gezelter	3021
223
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] = 4.0NumericConstant::PI/(RealType)(2*l + 1);
230			q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231			}
232	gezelter	3022
233			// Find second order invariant Q_l
234	gezelter	3021
235	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
236			q2[l] = 0.0;
237			for (int m = -l; m <= l; m++){
238			q2[l] += norm(q[std::make_pair(l,m)]);
239			}
240			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241			(RealType)(2*l + 1))/(RealType)nBonds;
242			}
243
244			// Find Third Order Invariant W_l
245
246			for (int l = 0; l <= lMax_; l++) {
247			w[l] = 0.0;
248			lPass = (double)l;
249			for (int m1 = -l; m1 <= l; m1++) {
250			// Zero work array
251			for (int ii = 0; ii < 2*l + 1; ii++){
252			THRCOF[ii] = 0.0;
253			}
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			}
269			}
270
271			w_hat[l] = w[l] / pow(q2[l], 1.5);
272			}
273
274			collectHistogram(q_l, w_hat);
275
276	gezelter	3017	Nbonds += nBonds;
277	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
278			for (int m = -l; m <= l; m++) {
279			QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
280			}
281	gezelter	3017	}
282			}
283	gezelter	3015	}
284	gezelter	3021
285	gezelter	3015	// Normalize Qbar2
286	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
287			for (int m = -l; m <= l; m++){
288			QBar[std::make_pair(l,m)] /= Nbonds;
289			}
290	gezelter	3007	}
291
292	gezelter	3015	// Find second order invariant Q_l
293	gezelter	3007
294	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
295			Q2[l] = 0.0;
296			for (int m = -l; m <= l; m++){
297			Q2[l] += norm(QBar[std::make_pair(l,m)]);
298			}
299			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
300	gezelter	3007	}
301	gezelter	3015
302			// Find Third Order Invariant W_l
303
304	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
305			W[l] = 0.0;
306			lPass = (double)l;
307			for (int m1 = -l; m1 <= l; m1++) {
308			// Zero work array
309			for (int ii = 0; ii < 2*l + 1; ii++){
310			THRCOF[ii] = 0.0;
311			}
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			}
327	gezelter	3015	}
328	gezelter	3009
329	gezelter	3021	W_hat[l] = W[l] / pow(Q2[l], 1.5);
330	gezelter	3007	}
331	gezelter	3015
332	gezelter	3021	writeOrderParameter(Q, W_hat);
333	gezelter	3015	}
334	chuckv	3005
335	gezelter	3022	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336			std::vector<ComplexType> what) {
337	chuckv	3005
338	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
339			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
340			int qbin = (q[l] - MinQ_) / deltaQ_;
341			Q_histogram_[std::make_pair(qbin,l)] += 1;
342			Qcount_[l]++;
343			} else {
344			sprintf( painCave.errMsg,
345			"q_l value outside reasonable range\n");
346			painCave.severity = OOPSE_ERROR;
347			painCave.isFatal = 1;
348			simError();
349			}
350	gezelter	3017	}
351
352	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
353			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
354			int wbin = (real(what[l]) - MinW_) / deltaW_;
355			W_histogram_[std::make_pair(wbin,l)] += 1;
356			Wcount_[l]++;
357			} else {
358			sprintf( painCave.errMsg,
359			"Re[w_hat] value outside reasonable range\n");
360			painCave.severity = OOPSE_ERROR;
361			painCave.isFatal = 1;
362			simError();
363			}
364			}
365
366	gezelter	3017	}
367
368
369	gezelter	3022	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370			std::vector<ComplexType> What) {
371	gezelter	3021
372	gezelter	3022	std::ofstream osq((getOutputFileName() + "q").c_str());
373
374			if (osq.is_open()) {
375	gezelter	3009
376	gezelter	3022	osq << "# Bond Order Parameters\n";
377			osq << "# selection: (" << selectionScript_ << ")\n";
378			osq << "# \n";
379	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
380	gezelter	3022	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
381	gezelter	3021	}
382	gezelter	3017	// Normalize by number of frames and write it out:
383	gezelter	3021	for (int i = 0; i < nBins_; ++i) {
384			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
385	gezelter	3022	osq << Qval;
386	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
387	gezelter	3022	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
388	gezelter	3021	}
389	gezelter	3022	osq << "\n";
390	gezelter	3017	}
391
392	gezelter	3022	osq.close();
393	gezelter	3015
394	gezelter	3009	} else {
395			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396	gezelter	3022	(getOutputFileName() + "q").c_str());
397	gezelter	3009	painCave.isFatal = 1;
398			simError();
399			}
400	gezelter	3022
401			std::ofstream osw((getOutputFileName() + "w").c_str());
402
403			if (osw.is_open()) {
404			osw << "# Bond Order Parameters\n";
405			osw << "# selection: (" << selectionScript_ << ")\n";
406			osw << "# \n";
407			for (int l = 0; l <= lMax_; l++) {
408			osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
409			}
410			// Normalize by number of frames and write it out:
411			for (int i = 0; i < nBins_; ++i) {
412			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
413			osw << Wval;
414			for (int l = 0; l <= lMax_; l++) {
415			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
416			}
417			osw << "\n";
418			}
419
420			osw.close();
421			} else {
422			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
423			(getOutputFileName() + "w").c_str());
424			painCave.isFatal = 1;
425			simError();
426			}
427
428	gezelter	3009	}
429	gezelter	3007	}