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 1.21 2006-11-21 20:44:54 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);
    Nbonds = 0;

    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();       

              if (usePeriodicBoundaryConditions_) 
                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++) {
          q2[l] = 0.0;
          for (int m = -l; m <= l; m++){
            q[std::make_pair(l,m)] /= (RealType)nBonds;            
            q2[l] += norm(q[std::make_pair(l,m)]);
          }
          q_l[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] * 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)] += (RealType)nBonds*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 (%lf) outside reasonable range\n", real(what[l]));
        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]/deltaQ_;
        }
        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]) << "\t" << imag(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]/deltaW_;
        }
        osw << "\n";
      }

      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
       
  }
}
Revision:	1094
Committed:	Tue Nov 21 20:44:54 2006 UTC (18 years, 5 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/BondOrderParameter.cpp*
File size:	13864 byte(s)
Log Message:	fixes for BOP
#	User	Rev	Content
1	chuckv	1038	/*
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	1054	*
41			* BondOrderParameter.cpp
42			* OOPSE-4
43			*
44			* Created by J. Daniel Gezelter on 09/26/06.
45			* @author J. Daniel Gezelter
46	gezelter	1094	* @version $Id: BondOrderParameter.cpp,v 1.21 2006-11-21 20:44:54 gezelter Exp $
47	gezelter	1054	*
48	chuckv	1038	*/
49	gezelter	1039
50	chuckv	1038	#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	1041
56	chuckv	1038	namespace oopse {
57
58	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	1052	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	1039
63	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	1038
65	gezelter	1039	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	1038	}
69
70	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	1038	rCut_ = rCut;
73	gezelter	1051	nBins_ = nbins;
74			Qcount_.resize(lMax_+1);
75			Wcount_.resize(lMax_+1);
76	gezelter	1048
77			// Q can take values from 0 to 1
78
79			MinQ_ = 0.0;
80	gezelter	1051	MaxQ_ = 1.1;
81	gezelter	1048	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	1052	MinW_ = -0.25;
87			MaxW_ = 0.25;
88	gezelter	1048	deltaW_ = (MaxW_ - MinW_) / nbins;
89	gezelter	1053
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	1054	delete [] THRCOF;
123			THRCOF = NULL;
124	gezelter	1039	}
125	gezelter	1053
126	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
127	gezelter	1048	Q_histogram_.clear();
128			W_histogram_.clear();
129	gezelter	1054	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	1041	}
138	gezelter	1054
139	gezelter	1048	void BondOrderParameter::initalizeHistogram() {
140	gezelter	1051	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	1048	}
147
148	gezelter	1039	void BondOrderParameter::process() {
149			Molecule* mol;
150			Atom* atom;
151			RigidBody* rb;
152	gezelter	1043	int myIndex;
153	gezelter	1039	SimInfo::MoleculeIterator mi;
154			Molecule::RigidBodyIterator rbIter;
155			Molecule::AtomIterator ai;
156			StuntDouble* sd;
157	gezelter	1043	Vector3d vec;
158	gezelter	1042	RealType costheta;
159	gezelter	1039	RealType phi;
160			RealType r;
161			RealType dist;
162	gezelter	1051	std::map<std::pair<int,int>,ComplexType> q;
163			std::vector<RealType> q_l;
164	gezelter	1052	std::vector<RealType> q2;
165			std::vector<ComplexType> w;
166			std::vector<ComplexType> w_hat;
167	gezelter	1051	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	1048	int nBonds, Nbonds;
173	gezelter	1042	SphericalHarmonic sphericalHarmonic;
174	gezelter	1039	int i, j;
175	gezelter	1043
176	gezelter	1039	DumpReader reader(info_, dumpFilename_);
177			int nFrames = reader.getNFrames();
178	gezelter	1041	frameCounter_ = 0;
179	chuckv	1038
180	gezelter	1051	q_l.resize(lMax_+1);
181	gezelter	1052	q2.resize(lMax_+1);
182			w.resize(lMax_+1);
183			w_hat.resize(lMax_+1);
184
185	gezelter	1051	Q2.resize(lMax_+1);
186			Q.resize(lMax_+1);
187			W.resize(lMax_+1);
188			W_hat.resize(lMax_+1);
189	gezelter	1094	Nbonds = 0;
190	gezelter	1051
191	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
192			reader.readFrame(istep);
193	gezelter	1041	frameCounter_++;
194	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
195
196			if (evaluator_.isDynamic()) {
197			seleMan_.setSelectionSet(evaluator_.evaluate());
198			}
199	chuckv	1038
200	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
201	chuckv	1038
202	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
203			mol = info_->nextMolecule(mi)) {
204			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
205			rb = mol->nextRigidBody(rbIter)) {
206			rb->updateAtoms();
207			}
208	gezelter	1048	}
209
210	gezelter	1039	// outer loop is over the selected StuntDoubles:
211	chuckv	1038
212	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
213			sd = seleMan_.nextSelected(i)) {
214	chuckv	1038
215	gezelter	1043	myIndex = sd->getGlobalIndex();
216	gezelter	1048	nBonds = 0;
217	gezelter	1051
218			for (int l = 0; l <= lMax_; l++) {
219			for (int m = -l; m <= l; m++) {
220			q[std::make_pair(l,m)] = 0.0;
221			}
222	gezelter	1048	}
223	gezelter	1039
224			// inner loop is over all other atoms in the system:
225
226			for (mol = info_->beginMolecule(mi); mol != NULL;
227			mol = info_->nextMolecule(mi)) {
228			for (atom = mol->beginAtom(ai); atom != NULL;
229			atom = mol->nextAtom(ai)) {
230	chuckv	1038
231	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
232	chuckv	1038
233	gezelter	1043	vec = sd->getPos() - atom->getPos();
234	gezelter	1078
235			if (usePeriodicBoundaryConditions_)
236			currentSnapshot_->wrapVector(vec);
237	gezelter	1042
238	gezelter	1043	// Calculate "bonds" and build Q_lm(r) where
239			// Q_lm = Y_lm(theta(r),phi(r))
240			// The spherical harmonics are wrt any arbitrary coordinate
241			// system, we choose standard spherical coordinates
242
243			r = vec.length();
244
245			// Check to see if neighbor is in bond cutoff
246
247			if (r < rCut_) {
248			costheta = vec.z() / r;
249			phi = atan2(vec.y(), vec.x());
250	gezelter	1051
251			for (int l = 0; l <= lMax_; l++) {
252			sphericalHarmonic.setL(l);
253			for(int m = -l; m <= l; m++){
254			sphericalHarmonic.setM(m);
255			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256			}
257	gezelter	1043	}
258			nBonds++;
259			}
260			}
261	gezelter	1039	}
262			}
263	gezelter	1051
264
265	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
266			q2[l] = 0.0;
267			for (int m = -l; m <= l; m++){
268	gezelter	1094	q[std::make_pair(l,m)] /= (RealType)nBonds;
269	gezelter	1052	q2[l] += norm(q[std::make_pair(l,m)]);
270			}
271	gezelter	1094	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
272	gezelter	1052	}
273	gezelter	1094
274	gezelter	1052	// Find Third Order Invariant W_l
275
276			for (int l = 0; l <= lMax_; l++) {
277			w[l] = 0.0;
278			for (int m1 = -l; m1 <= l; m1++) {
279	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
280			for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
281			int m2 = m2Min[lm] + mmm;
282			int m3 = -m1-m2;
283			w[l] += w3j[lm][mmm] * q[lm] *
284			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
285	gezelter	1052	}
286			}
287
288			w_hat[l] = w[l] / pow(q2[l], 1.5);
289			}
290
291			collectHistogram(q_l, w_hat);
292
293	gezelter	1048	Nbonds += nBonds;
294	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
295			for (int m = -l; m <= l; m++) {
296	gezelter	1094	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
297	gezelter	1051	}
298	gezelter	1048	}
299			}
300	gezelter	1047	}
301	gezelter	1051
302	gezelter	1047	// Normalize Qbar2
303	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
304			for (int m = -l; m <= l; m++){
305			QBar[std::make_pair(l,m)] /= Nbonds;
306			}
307	gezelter	1039	}
308
309	gezelter	1047	// Find second order invariant Q_l
310	gezelter	1039
311	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
312			Q2[l] = 0.0;
313			for (int m = -l; m <= l; m++){
314			Q2[l] += norm(QBar[std::make_pair(l,m)]);
315			}
316			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317	gezelter	1039	}
318	gezelter	1047
319			// Find Third Order Invariant W_l
320
321	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
322			W[l] = 0.0;
323			for (int m1 = -l; m1 <= l; m1++) {
324	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
325			for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
326			int m2 = m2Min[lm] + mmm;
327			int m3 = -m1-m2;
328			W[l] += w3j[lm][mmm] * QBar[lm] *
329			QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
330	gezelter	1051	}
331	gezelter	1047	}
332	gezelter	1041
333	gezelter	1051	W_hat[l] = W[l] / pow(Q2[l], 1.5);
334	gezelter	1039	}
335	gezelter	1047
336	gezelter	1051	writeOrderParameter(Q, W_hat);
337	gezelter	1047	}
338	chuckv	1038
339	gezelter	1052	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340			std::vector<ComplexType> what) {
341	chuckv	1038
342	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
343			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344			int qbin = (q[l] - MinQ_) / deltaQ_;
345			Q_histogram_[std::make_pair(qbin,l)] += 1;
346			Qcount_[l]++;
347			} else {
348			sprintf( painCave.errMsg,
349			"q_l value outside reasonable range\n");
350			painCave.severity = OOPSE_ERROR;
351			painCave.isFatal = 1;
352			simError();
353			}
354	gezelter	1048	}
355
356	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
357			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358			int wbin = (real(what[l]) - MinW_) / deltaW_;
359			W_histogram_[std::make_pair(wbin,l)] += 1;
360			Wcount_[l]++;
361			} else {
362			sprintf( painCave.errMsg,
363	gezelter	1094	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
364	gezelter	1052	painCave.severity = OOPSE_ERROR;
365			painCave.isFatal = 1;
366			simError();
367			}
368			}
369
370	gezelter	1048	}
371
372
373	gezelter	1052	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374			std::vector<ComplexType> What) {
375	gezelter	1051
376	gezelter	1052	std::ofstream osq((getOutputFileName() + "q").c_str());
377
378			if (osq.is_open()) {
379	gezelter	1041
380	gezelter	1052	osq << "# Bond Order Parameters\n";
381			osq << "# selection: (" << selectionScript_ << ")\n";
382			osq << "# \n";
383	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
384	gezelter	1052	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385	gezelter	1051	}
386	gezelter	1048	// Normalize by number of frames and write it out:
387	gezelter	1051	for (int i = 0; i < nBins_; ++i) {
388			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
389	gezelter	1052	osq << Qval;
390	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
391	gezelter	1094
392			osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393	gezelter	1051	}
394	gezelter	1052	osq << "\n";
395	gezelter	1048	}
396
397	gezelter	1052	osq.close();
398	gezelter	1047
399	gezelter	1041	} else {
400			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401	gezelter	1052	(getOutputFileName() + "q").c_str());
402	gezelter	1041	painCave.isFatal = 1;
403			simError();
404			}
405	gezelter	1052
406			std::ofstream osw((getOutputFileName() + "w").c_str());
407
408			if (osw.is_open()) {
409			osw << "# Bond Order Parameters\n";
410			osw << "# selection: (" << selectionScript_ << ")\n";
411			osw << "# \n";
412			for (int l = 0; l <= lMax_; l++) {
413	gezelter	1090	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
414	gezelter	1052	}
415			// Normalize by number of frames and write it out:
416			for (int i = 0; i < nBins_; ++i) {
417			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
418			osw << Wval;
419			for (int l = 0; l <= lMax_; l++) {
420	gezelter	1094
421			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422	gezelter	1052	}
423			osw << "\n";
424			}
425
426			osw.close();
427			} else {
428			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
429			(getOutputFileName() + "w").c_str());
430			painCave.isFatal = 1;
431			simError();
432			}
433
434	gezelter	1041	}
435	gezelter	1039	}