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.
 *
 *  BondOrderParameter.cpp
 *  OOPSE-4
 *
 *  Created by J. Daniel Gezelter on 09/26/06.
 *  @author  J. Daniel Gezelter
 *  @version $Id: BondOrderParameter.cpp,v 1.18 2006-09-26 16:08:44 gezelter Exp $
 *
 */
 
#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]);
        }
      }
    }
    delete [] THRCOF;
    THRCOF = NULL;
  }
  
  BondOrderParameter::~BondOrderParameter() {
    Q_histogram_.clear();
    W_histogram_.clear();
    for (int l = 0; l <= lMax_; l++) {
      for (int m = -l; m <= l; m++) {
        w3j[std::make_pair(l,m)].clear();
      }
    }
    w3j.clear();
    m2Min.clear();
    m2Max.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:	3026
Committed:	Tue Sep 26 16:08:44 2006 UTC (17 years, 9 months ago) by gezelter
File size:	14074 byte(s)
Log Message:	Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten.
#	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	gezelter	3026	*
41			* BondOrderParameter.cpp
42			* OOPSE-4
43			*
44			* Created by J. Daniel Gezelter on 09/26/06.
45			* @author J. Daniel Gezelter
46			* @version $Id: BondOrderParameter.cpp,v 1.18 2006-09-26 16:08:44 gezelter Exp $
47			*
48	chuckv	3005	*/
49	gezelter	3007
50	chuckv	3005	#include "applications/staticProps/BondOrderParameter.hpp"
51			#include "utils/simError.h"
52			#include "io/DumpReader.hpp"
53			#include "primitives/Molecule.hpp"
54			#include "utils/NumericConstant.hpp"
55	gezelter	3009
56	chuckv	3005	namespace oopse {
57
58	gezelter	3007	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	3022	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	3007
63	gezelter	3009	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	3005
65	gezelter	3007	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	3005	}
69
70	gezelter	3007	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	3005	rCut_ = rCut;
73	gezelter	3021	nBins_ = nbins;
74			Qcount_.resize(lMax_+1);
75			Wcount_.resize(lMax_+1);
76	gezelter	3017
77			// Q can take values from 0 to 1
78
79			MinQ_ = 0.0;
80	gezelter	3021	MaxQ_ = 1.1;
81	gezelter	3017	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
82
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	gezelter	3022	MinW_ = -0.25;
87			MaxW_ = 0.25;
88	gezelter	3017	deltaW_ = (MaxW_ - MinW_) / nbins;
89	gezelter	3024
90			// Make arrays for Wigner3jm
91			double* THRCOF = new double[2*lMax_+1];
92			// Variables for Wigner routine
93			double lPass, m1Pass, m2m, m2M;
94			int error, mSize;
95			mSize = 2*lMax_+1;
96
97			for (int l = 0; l <= lMax_; l++) {
98			lPass = (double)l;
99			for (int m1 = -l; m1 <= l; m1++) {
100			m1Pass = (double)m1;
101
102			std::pair<int,int> lm = std::make_pair(l, m1);
103
104			// Zero work array
105			for (int ii = 0; ii < 2*l + 1; ii++){
106			THRCOF[ii] = 0.0;
107			}
108
109			// Get Wigner coefficients
110			Wigner3jm(&lPass, &lPass, &lPass,
111			&m1Pass, &m2m, &m2M,
112			THRCOF, &mSize, &error);
113
114			m2Min[lm] = (int)floor(m2m);
115			m2Max[lm] = (int)floor(m2M);
116
117			for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
118			w3j[lm].push_back(THRCOF[mmm]);
119			}
120			}
121			}
122	gezelter	3026	delete [] THRCOF;
123			THRCOF = NULL;
124	gezelter	3007	}
125	gezelter	3024
126	gezelter	3009	BondOrderParameter::~BondOrderParameter() {
127	gezelter	3017	Q_histogram_.clear();
128			W_histogram_.clear();
129	gezelter	3026	for (int l = 0; l <= lMax_; l++) {
130			for (int m = -l; m <= l; m++) {
131			w3j[std::make_pair(l,m)].clear();
132			}
133			}
134			w3j.clear();
135			m2Min.clear();
136			m2Max.clear();
137	gezelter	3009	}
138	gezelter	3026
139	gezelter	3017	void BondOrderParameter::initalizeHistogram() {
140	gezelter	3021	for (int bin = 0; bin < nBins_; bin++) {
141			for (int l = 0; l <= lMax_; l++) {
142			Q_histogram_[std::make_pair(bin,l)] = 0;
143			W_histogram_[std::make_pair(bin,l)] = 0;
144			}
145			}
146	gezelter	3017	}
147
148	gezelter	3007	void BondOrderParameter::process() {
149			Molecule* mol;
150			Atom* atom;
151			RigidBody* rb;
152	gezelter	3011	int myIndex;
153	gezelter	3007	SimInfo::MoleculeIterator mi;
154			Molecule::RigidBodyIterator rbIter;
155			Molecule::AtomIterator ai;
156			StuntDouble* sd;
157	gezelter	3011	Vector3d vec;
158	gezelter	3010	RealType costheta;
159	gezelter	3007	RealType phi;
160			RealType r;
161			RealType dist;
162	gezelter	3021	std::map<std::pair<int,int>,ComplexType> q;
163			std::vector<RealType> q_l;
164	gezelter	3022	std::vector<RealType> q2;
165			std::vector<ComplexType> w;
166			std::vector<ComplexType> w_hat;
167	gezelter	3021	std::map<std::pair<int,int>,ComplexType> QBar;
168			std::vector<RealType> Q2;
169			std::vector<RealType> Q;
170			std::vector<ComplexType> W;
171			std::vector<ComplexType> W_hat;
172	gezelter	3017	int nBonds, Nbonds;
173	gezelter	3010	SphericalHarmonic sphericalHarmonic;
174	gezelter	3007	int i, j;
175	gezelter	3011
176	gezelter	3007	DumpReader reader(info_, dumpFilename_);
177			int nFrames = reader.getNFrames();
178	gezelter	3009	frameCounter_ = 0;
179	chuckv	3005
180	gezelter	3021	q_l.resize(lMax_+1);
181	gezelter	3022	q2.resize(lMax_+1);
182			w.resize(lMax_+1);
183			w_hat.resize(lMax_+1);
184
185	gezelter	3021	Q2.resize(lMax_+1);
186			Q.resize(lMax_+1);
187			W.resize(lMax_+1);
188			W_hat.resize(lMax_+1);
189
190	gezelter	3007	for (int istep = 0; istep < nFrames; istep += step_) {
191			reader.readFrame(istep);
192	gezelter	3009	frameCounter_++;
193	gezelter	3007	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
194
195			if (evaluator_.isDynamic()) {
196			seleMan_.setSelectionSet(evaluator_.evaluate());
197			}
198	chuckv	3005
199	gezelter	3007	// update the positions of atoms which belong to the rigidbodies
200	chuckv	3005
201	gezelter	3007	for (mol = info_->beginMolecule(mi); mol != NULL;
202			mol = info_->nextMolecule(mi)) {
203			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
204			rb = mol->nextRigidBody(rbIter)) {
205			rb->updateAtoms();
206			}
207	gezelter	3017	}
208
209	gezelter	3007	// outer loop is over the selected StuntDoubles:
210	chuckv	3005
211	gezelter	3007	for (sd = seleMan_.beginSelected(i); sd != NULL;
212			sd = seleMan_.nextSelected(i)) {
213	chuckv	3005
214	gezelter	3011	myIndex = sd->getGlobalIndex();
215	gezelter	3017	nBonds = 0;
216	gezelter	3021
217			for (int l = 0; l <= lMax_; l++) {
218			for (int m = -l; m <= l; m++) {
219			q[std::make_pair(l,m)] = 0.0;
220			}
221	gezelter	3017	}
222	gezelter	3007
223			// inner loop is over all other atoms in the system:
224
225			for (mol = info_->beginMolecule(mi); mol != NULL;
226			mol = info_->nextMolecule(mi)) {
227			for (atom = mol->beginAtom(ai); atom != NULL;
228			atom = mol->nextAtom(ai)) {
229	chuckv	3005
230	gezelter	3011	if (atom->getGlobalIndex() != myIndex) {
231	chuckv	3005
232	gezelter	3011	vec = sd->getPos() - atom->getPos();
233			currentSnapshot_->wrapVector(vec);
234	gezelter	3010
235	gezelter	3011	// Calculate "bonds" and build Q_lm(r) where
236			// Q_lm = Y_lm(theta(r),phi(r))
237			// The spherical harmonics are wrt any arbitrary coordinate
238			// system, we choose standard spherical coordinates
239
240			r = vec.length();
241
242			// Check to see if neighbor is in bond cutoff
243
244			if (r < rCut_) {
245			costheta = vec.z() / r;
246			phi = atan2(vec.y(), vec.x());
247	gezelter	3021
248			for (int l = 0; l <= lMax_; l++) {
249			sphericalHarmonic.setL(l);
250			for(int m = -l; m <= l; m++){
251			sphericalHarmonic.setM(m);
252			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
253			}
254	gezelter	3011	}
255			nBonds++;
256			}
257			}
258	gezelter	3007	}
259			}
260	gezelter	3021
261
262			for (int l = 0; l <= lMax_; l++) {
263			q_l[l] = 0.0;
264			for(int m = -l; m <= l; m++) {
265			q_l[l] += norm(q[std::make_pair(l,m)]);
266			}
267			q_l[l] = 4.0NumericConstant::PI/(RealType)(2*l + 1);
268			q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
269			}
270	gezelter	3022
271			// Find second order invariant Q_l
272	gezelter	3021
273	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
274			q2[l] = 0.0;
275			for (int m = -l; m <= l; m++){
276			q2[l] += norm(q[std::make_pair(l,m)]);
277			}
278			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
279			(RealType)(2*l + 1))/(RealType)nBonds;
280			}
281
282			// Find Third Order Invariant W_l
283
284			for (int l = 0; l <= lMax_; l++) {
285			w[l] = 0.0;
286			for (int m1 = -l; m1 <= l; m1++) {
287	gezelter	3024	std::pair<int,int> lm = std::make_pair(l, m1);
288			for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
289			int m2 = m2Min[lm] + mmm;
290			int m3 = -m1-m2;
291			w[l] += w3j[lm][mmm] * q[lm] *
292			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
293	gezelter	3022	}
294			}
295
296			w_hat[l] = w[l] / pow(q2[l], 1.5);
297			}
298
299			collectHistogram(q_l, w_hat);
300
301	gezelter	3017	Nbonds += nBonds;
302	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
303			for (int m = -l; m <= l; m++) {
304			QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
305			}
306	gezelter	3017	}
307			}
308	gezelter	3015	}
309	gezelter	3021
310	gezelter	3015	// Normalize Qbar2
311	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
312			for (int m = -l; m <= l; m++){
313			QBar[std::make_pair(l,m)] /= Nbonds;
314			}
315	gezelter	3007	}
316
317	gezelter	3015	// Find second order invariant Q_l
318	gezelter	3007
319	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
320			Q2[l] = 0.0;
321			for (int m = -l; m <= l; m++){
322			Q2[l] += norm(QBar[std::make_pair(l,m)]);
323			}
324			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
325	gezelter	3007	}
326	gezelter	3015
327			// Find Third Order Invariant W_l
328
329	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
330			W[l] = 0.0;
331			for (int m1 = -l; m1 <= l; m1++) {
332	gezelter	3024	std::pair<int,int> lm = std::make_pair(l, m1);
333			for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
334			int m2 = m2Min[lm] + mmm;
335			int m3 = -m1-m2;
336			W[l] += w3j[lm][mmm] * QBar[lm] *
337			QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
338	gezelter	3021	}
339	gezelter	3015	}
340	gezelter	3009
341	gezelter	3021	W_hat[l] = W[l] / pow(Q2[l], 1.5);
342	gezelter	3007	}
343	gezelter	3015
344	gezelter	3021	writeOrderParameter(Q, W_hat);
345	gezelter	3015	}
346	chuckv	3005
347	gezelter	3022	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
348			std::vector<ComplexType> what) {
349	chuckv	3005
350	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
351			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
352			int qbin = (q[l] - MinQ_) / deltaQ_;
353			Q_histogram_[std::make_pair(qbin,l)] += 1;
354			Qcount_[l]++;
355			} else {
356			sprintf( painCave.errMsg,
357			"q_l value outside reasonable range\n");
358			painCave.severity = OOPSE_ERROR;
359			painCave.isFatal = 1;
360			simError();
361			}
362	gezelter	3017	}
363
364	gezelter	3022	for (int l = 0; l <= lMax_; l++) {
365			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
366			int wbin = (real(what[l]) - MinW_) / deltaW_;
367			W_histogram_[std::make_pair(wbin,l)] += 1;
368			Wcount_[l]++;
369			} else {
370			sprintf( painCave.errMsg,
371			"Re[w_hat] value outside reasonable range\n");
372			painCave.severity = OOPSE_ERROR;
373			painCave.isFatal = 1;
374			simError();
375			}
376			}
377
378	gezelter	3017	}
379
380
381	gezelter	3022	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
382			std::vector<ComplexType> What) {
383	gezelter	3021
384	gezelter	3022	std::ofstream osq((getOutputFileName() + "q").c_str());
385
386			if (osq.is_open()) {
387	gezelter	3009
388	gezelter	3022	osq << "# Bond Order Parameters\n";
389			osq << "# selection: (" << selectionScript_ << ")\n";
390			osq << "# \n";
391	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
392	gezelter	3022	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
393	gezelter	3021	}
394	gezelter	3017	// Normalize by number of frames and write it out:
395	gezelter	3021	for (int i = 0; i < nBins_; ++i) {
396			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
397	gezelter	3022	osq << Qval;
398	gezelter	3021	for (int l = 0; l <= lMax_; l++) {
399	gezelter	3026	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] /
400			(RealType)Qcount_[l];
401	gezelter	3021	}
402	gezelter	3022	osq << "\n";
403	gezelter	3017	}
404
405	gezelter	3022	osq.close();
406	gezelter	3015
407	gezelter	3009	} else {
408			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
409	gezelter	3022	(getOutputFileName() + "q").c_str());
410	gezelter	3009	painCave.isFatal = 1;
411			simError();
412			}
413	gezelter	3022
414			std::ofstream osw((getOutputFileName() + "w").c_str());
415
416			if (osw.is_open()) {
417			osw << "# Bond Order Parameters\n";
418			osw << "# selection: (" << selectionScript_ << ")\n";
419			osw << "# \n";
420			for (int l = 0; l <= lMax_; l++) {
421			osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
422			}
423			// Normalize by number of frames and write it out:
424			for (int i = 0; i < nBins_; ++i) {
425			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
426			osw << Wval;
427			for (int l = 0; l <= lMax_; l++) {
428	gezelter	3026	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] /
429			(RealType)Wcount_[l];
430	gezelter	3022	}
431			osw << "\n";
432			}
433
434			osw.close();
435			} else {
436			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
437			(getOutputFileName() + "w").c_str());
438			painCave.isFatal = 1;
439			simError();
440			}
441
442	gezelter	3009	}
443	gezelter	3007	}