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;

    // Make arrays for Wigner3jm
    double* THRCOF = new double[2*lMax_+1];
    // Variables for Wigner routine
    double lPass, m1Pass, m2m, m2M;
    int error, mSize;
    mSize = 2*lMax_+1;

    for (int l = 0; l <= lMax_; l++) {
      lPass = (double)l;
      for (int m1 = -l; m1 <= l; m1++) {
        m1Pass = (double)m1;

        std::pair<int,int> lm = std::make_pair(l, m1);
        
        // Zero work array
        for (int ii = 0; ii < 2*l + 1; ii++){
          THRCOF[ii] = 0.0;
        }
            
        // Get Wigner coefficients
        Wigner3jm(&lPass, &lPass, &lPass, 
                  &m1Pass, &m2m, &m2M, 
                  THRCOF, &mSize, &error);
        
        m2Min[lm] = (int)floor(m2m);
        m2Max[lm] = (int)floor(m2M);
        
        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
          w3j[lm].push_back(THRCOF[mmm]);
        }
      }
    }
  }
  
  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;

    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;
          for (int m1 = -l; m1 <= l; m1++) {
            std::pair<int,int> lm = std::make_pair(l, m1);
            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
              int m2 = m2Min[lm] + mmm;
              int m3 = -m1-m2;
              w[l] += w3j[lm][mmm] * q[lm] * 
                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;
      for (int m1 = -l; m1 <= l; m1++) {
        std::pair<int,int> lm = std::make_pair(l, m1);
        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
          int m2 = m2Min[lm] + mmm;
          int m3 = -m1-m2;
          W[l] += w3j[lm][mmm] * QBar[lm] * 
            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:	3024
Committed:	Tue Sep 26 14:33:56 2006 UTC (17 years, 9 months ago) by gezelter
File size:	13792 byte(s)
Log Message:	Some efficiency fixes (now computes Wigner 3-j coefficients only once in the constructor).
#	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	3024
89			// Make arrays for Wigner3jm
90			double* THRCOF = new double[2*lMax_+1];
91			// Variables for Wigner routine
92			double lPass, m1Pass, m2m, m2M;
93			int error, mSize;
94			mSize = 2*lMax_+1;
95
96			for (int l = 0; l <= lMax_; l++) {
97			lPass = (double)l;
98			for (int m1 = -l; m1 <= l; m1++) {
99			m1Pass = (double)m1;
100
101			std::pair<int,int> lm = std::make_pair(l, m1);
102
103			// Zero work array
104			for (int ii = 0; ii < 2*l + 1; ii++){
105			THRCOF[ii] = 0.0;
106			}
107
108			// Get Wigner coefficients
109			Wigner3jm(&lPass, &lPass, &lPass,
110			&m1Pass, &m2m, &m2M,
111			THRCOF, &mSize, &error);
112
113			m2Min[lm] = (int)floor(m2m);
114			m2Max[lm] = (int)floor(m2M);
115
116			for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
117			w3j[lm].push_back(THRCOF[mmm]);
118			}
119			}
120			}
121	gezelter	3007	}
122	gezelter	3024
123	gezelter	3009	BondOrderParameter::~BondOrderParameter() {
124	gezelter	3017	Q_histogram_.clear();
125			W_histogram_.clear();
126	gezelter	3009	}
127
128	gezelter	3017	void BondOrderParameter::initalizeHistogram() {
129	gezelter	3021	for (int bin = 0; bin < nBins_; bin++) {
130			for (int l = 0; l <= lMax_; l++) {
131			Q_histogram_[std::make_pair(bin,l)] = 0;
132			W_histogram_[std::make_pair(bin,l)] = 0;
133			}
134			}
135	gezelter	3017	}
136
137	gezelter	3007	void BondOrderParameter::process() {
138			Molecule* mol;
139			Atom* atom;
140			RigidBody* rb;
141	gezelter	3011	int myIndex;
142	gezelter	3007	SimInfo::MoleculeIterator mi;
143			Molecule::RigidBodyIterator rbIter;
144			Molecule::AtomIterator ai;
145			StuntDouble* sd;
146	gezelter	3011	Vector3d vec;
147	gezelter	3010	RealType costheta;
148	gezelter	3007	RealType phi;
149			RealType r;
150			RealType dist;
151	gezelter	3021	std::map<std::pair<int,int>,ComplexType> q;
152			std::vector<RealType> q_l;
153	gezelter	3022	std::vector<RealType> q2;
154			std::vector<ComplexType> w;
155			std::vector<ComplexType> w_hat;
156	gezelter	3021	std::map<std::pair<int,int>,ComplexType> QBar;
157			std::vector<RealType> Q2;
158			std::vector<RealType> Q;
159			std::vector<ComplexType> W;
160			std::vector<ComplexType> W_hat;
161	gezelter	3017	int nBonds, Nbonds;
162	gezelter	3010	SphericalHarmonic sphericalHarmonic;
163	gezelter	3007	int i, j;
164	gezelter	3011
165	gezelter	3007	DumpReader reader(info_, dumpFilename_);
166			int nFrames = reader.getNFrames();
167	gezelter	3009	frameCounter_ = 0;
168	chuckv	3005
169	gezelter	3021	q_l.resize(lMax_+1);
170	gezelter	3022	q2.resize(lMax_+1);
171			w.resize(lMax_+1);
172			w_hat.resize(lMax_+1);
173
174	gezelter	3021	Q2.resize(lMax_+1);
175			Q.resize(lMax_+1);
176			W.resize(lMax_+1);
177			W_hat.resize(lMax_+1);
178
179	gezelter	3007	for (int istep = 0; istep < nFrames; istep += step_) {
180			reader.readFrame(istep);
181	gezelter	3009	frameCounter_++;
182	gezelter	3007	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
183
184			if (evaluator_.isDynamic()) {
185			seleMan_.setSelectionSet(evaluator_.evaluate());
186			}
187	chuckv	3005
188	gezelter	3007	// update the positions of atoms which belong to the rigidbodies
189	chuckv	3005
190	gezelter	3007	for (mol = info_->beginMolecule(mi); mol != NULL;
191			mol = info_->nextMolecule(mi)) {
192			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
193			rb = mol->nextRigidBody(rbIter)) {
194			rb->updateAtoms();
195			}
196	gezelter	3017	}
197
198	gezelter	3007	// outer loop is over the selected StuntDoubles:
199	chuckv	3005
200	gezelter	3007	for (sd = seleMan_.beginSelected(i); sd != NULL;
201			sd = seleMan_.nextSelected(i)) {
202	chuckv	3005
203	gezelter	3011	myIndex = sd->getGlobalIndex();
204	gezelter	3017	nBonds = 0;
205	gezelter	3021
206			for (int l = 0; l <= lMax_; l++) {
207			for (int m = -l; m <= l; m++) {
208			q[std::make_pair(l,m)] = 0.0;
209			}
210	gezelter	3017	}
211	gezelter	3007
212			// inner loop is over all other atoms in the system:
213
214			for (mol = info_->beginMolecule(mi); mol != NULL;
215			mol = info_->nextMolecule(mi)) {
216			for (atom = mol->beginAtom(ai); atom != NULL;
217			atom = mol->nextAtom(ai)) {
218	chuckv	3005
219	gezelter	3011	if (atom->getGlobalIndex() != myIndex) {
220	chuckv	3005
221	gezelter	3011	vec = sd->getPos() - atom->getPos();
222			currentSnapshot_->wrapVector(vec);
223	gezelter	3010
224	gezelter	3011	// Calculate "bonds" and build Q_lm(r) where
225			// Q_lm = Y_lm(theta(r),phi(r))
226			// The spherical harmonics are wrt any arbitrary coordinate
227			// system, we choose standard spherical coordinates
228
229			r = vec.length();
230
231			// Check to see if neighbor is in bond cutoff
232
233			if (r < rCut_) {
234			costheta = vec.z() / r;
235			phi = atan2(vec.y(), vec.x());
236	gezelter	3021
237			for (int l = 0; l <= lMax_; l++) {
238			sphericalHarmonic.setL(l);
239			for(int m = -l; m <= l; m++){
240			sphericalHarmonic.setM(m);
241			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
242			}
243	gezelter	3011	}
244			nBonds++;
245			}
246			}
247	gezelter	3007	}
248			}
249	gezelter	3021
250
251			for (int l = 0; l <= lMax_; l++) {
252			q_l[l] = 0.0;
253			for(int m = -l; m <= l; m++) {
254			q_l[l] += norm(q[std::make_pair(l,m)]);
255			}
256			q_l[l] = 4.0NumericConstant::PI/(RealType)(2*l + 1);
257			q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
258			}
259	gezelter	3022
260			// Find second order invariant Q_l
261	gezelter	3021
262	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
263			q2[l] = 0.0;
264			for (int m = -l; m <= l; m++){
265			q2[l] += norm(q[std::make_pair(l,m)]);
266			}
267			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
268			(RealType)(2*l + 1))/(RealType)nBonds;
269			}
270
271			// Find Third Order Invariant W_l
272
273			for (int l = 0; l <= lMax_; l++) {
274			w[l] = 0.0;
275			for (int m1 = -l; m1 <= l; m1++) {
276	gezelter	3024	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	gezelter	3022	}
283			}
284
285			w_hat[l] = w[l] / pow(q2[l], 1.5);
286			}
287
288			collectHistogram(q_l, w_hat);
289
290	gezelter	3017	Nbonds += nBonds;
291	gezelter	3021	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)];
294			}
295	gezelter	3017	}
296			}
297	gezelter	3015	}
298	gezelter	3021
299	gezelter	3015	// Normalize Qbar2
300	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
301			for (int m = -l; m <= l; m++){
302			QBar[std::make_pair(l,m)] /= Nbonds;
303			}
304	gezelter	3007	}
305
306	gezelter	3015	// Find second order invariant Q_l
307	gezelter	3007
308	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
309			Q2[l] = 0.0;
310			for (int m = -l; m <= l; m++){
311			Q2[l] += norm(QBar[std::make_pair(l,m)]);
312			}
313			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
314	gezelter	3007	}
315	gezelter	3015
316			// Find Third Order Invariant W_l
317
318	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
319			W[l] = 0.0;
320			for (int m1 = -l; m1 <= l; m1++) {
321	gezelter	3024	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	gezelter	3021	}
328	gezelter	3015	}
329	gezelter	3009
330	gezelter	3021	W_hat[l] = W[l] / pow(Q2[l], 1.5);
331	gezelter	3007	}
332	gezelter	3015
333	gezelter	3021	writeOrderParameter(Q, W_hat);
334	gezelter	3015	}
335	chuckv	3005
336	gezelter	3022	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337			std::vector<ComplexType> what) {
338	chuckv	3005
339	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
340			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
341			int qbin = (q[l] - MinQ_) / deltaQ_;
342			Q_histogram_[std::make_pair(qbin,l)] += 1;
343			Qcount_[l]++;
344			} else {
345			sprintf( painCave.errMsg,
346			"q_l value outside reasonable range\n");
347			painCave.severity = OOPSE_ERROR;
348			painCave.isFatal = 1;
349			simError();
350			}
351	gezelter	3017	}
352
353	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
354			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
355			int wbin = (real(what[l]) - MinW_) / deltaW_;
356			W_histogram_[std::make_pair(wbin,l)] += 1;
357			Wcount_[l]++;
358			} else {
359			sprintf( painCave.errMsg,
360			"Re[w_hat] value outside reasonable range\n");
361			painCave.severity = OOPSE_ERROR;
362			painCave.isFatal = 1;
363			simError();
364			}
365			}
366
367	gezelter	3017	}
368
369
370	gezelter	3022	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371			std::vector<ComplexType> What) {
372	gezelter	3021
373	gezelter	3022	std::ofstream osq((getOutputFileName() + "q").c_str());
374
375			if (osq.is_open()) {
376	gezelter	3009
377	gezelter	3022	osq << "# Bond Order Parameters\n";
378			osq << "# selection: (" << selectionScript_ << ")\n";
379			osq << "# \n";
380	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
381	gezelter	3022	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
382	gezelter	3021	}
383	gezelter	3017	// Normalize by number of frames and write it out:
384	gezelter	3021	for (int i = 0; i < nBins_; ++i) {
385			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386	gezelter	3022	osq << Qval;
387	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
388	gezelter	3022	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
389	gezelter	3021	}
390	gezelter	3022	osq << "\n";
391	gezelter	3017	}
392
393	gezelter	3022	osq.close();
394	gezelter	3015
395	gezelter	3009	} else {
396			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
397	gezelter	3022	(getOutputFileName() + "q").c_str());
398	gezelter	3009	painCave.isFatal = 1;
399			simError();
400			}
401	gezelter	3022
402			std::ofstream osw((getOutputFileName() + "w").c_str());
403
404			if (osw.is_open()) {
405			osw << "# Bond Order Parameters\n";
406			osw << "# selection: (" << selectionScript_ << ")\n";
407			osw << "# \n";
408			for (int l = 0; l <= lMax_; l++) {
409			osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
410			}
411			// Normalize by number of frames and write it out:
412			for (int i = 0; i < nBins_; ++i) {
413			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
414			osw << Wval;
415			for (int l = 0; l <= lMax_; l++) {
416			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
417			}
418			osw << "\n";
419			}
420
421			osw.close();
422			} else {
423			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
424			(getOutputFileName() + "w").c_str());
425			painCave.isFatal = 1;
426			simError();
427			}
428
429	gezelter	3009	}
430	gezelter	3007	}