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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  Created by J. Daniel Gezelter on 09/26/06.
 *  @author  J. Daniel Gezelter
 *  @version $Id$
 *
 */
 
#include "applications/staticProps/BondOrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

namespace OpenMD {

  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_ = -1.1;
    MaxW_ = 1.1;
    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 = OPENMD_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 = OPENMD_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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	13790 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1038	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1038	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1054	*
32	gezelter	1390	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	1054	*
41			* Created by J. Daniel Gezelter on 09/26/06.
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	gezelter	1054	*
45	chuckv	1038	*/
46	gezelter	1039
47	chuckv	1038	#include "applications/staticProps/BondOrderParameter.hpp"
48			#include "utils/simError.h"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51			#include "utils/NumericConstant.hpp"
52	gezelter	1041
53	gezelter	1390	namespace OpenMD {
54	chuckv	1038
55	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
56			const std::string& filename,
57			const std::string& sele,
58	gezelter	1052	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
59	gezelter	1039
60	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
61	chuckv	1038
62	gezelter	1039	evaluator_.loadScriptString(sele);
63			if (!evaluator_.isDynamic()) {
64			seleMan_.setSelectionSet(evaluator_.evaluate());
65	chuckv	1038	}
66
67	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
68
69	chuckv	1038	rCut_ = rCut;
70	gezelter	1051	nBins_ = nbins;
71			Qcount_.resize(lMax_+1);
72			Wcount_.resize(lMax_+1);
73	gezelter	1048
74			// Q can take values from 0 to 1
75
76			MinQ_ = 0.0;
77	gezelter	1051	MaxQ_ = 1.1;
78	gezelter	1048	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
79
80			// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
81			// use values for MinW_ and MaxW_ that are slightly larger than this:
82
83	gezelter	1100	MinW_ = -1.1;
84			MaxW_ = 1.1;
85	gezelter	1048	deltaW_ = (MaxW_ - MinW_) / nbins;
86	gezelter	1053
87			// Make arrays for Wigner3jm
88			double* THRCOF = new double[2*lMax_+1];
89			// Variables for Wigner routine
90			double lPass, m1Pass, m2m, m2M;
91			int error, mSize;
92			mSize = 2*lMax_+1;
93
94			for (int l = 0; l <= lMax_; l++) {
95			lPass = (double)l;
96			for (int m1 = -l; m1 <= l; m1++) {
97			m1Pass = (double)m1;
98
99			std::pair<int,int> lm = std::make_pair(l, m1);
100
101			// Zero work array
102			for (int ii = 0; ii < 2*l + 1; ii++){
103			THRCOF[ii] = 0.0;
104			}
105	gezelter	1100
106	gezelter	1053	// Get Wigner coefficients
107			Wigner3jm(&lPass, &lPass, &lPass,
108			&m1Pass, &m2m, &m2M,
109			THRCOF, &mSize, &error);
110
111			m2Min[lm] = (int)floor(m2m);
112			m2Max[lm] = (int)floor(m2M);
113
114	gezelter	1100	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
115	gezelter	1053	w3j[lm].push_back(THRCOF[mmm]);
116			}
117			}
118			}
119	gezelter	1054	delete [] THRCOF;
120			THRCOF = NULL;
121	gezelter	1039	}
122	gezelter	1053
123	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
124	gezelter	1048	Q_histogram_.clear();
125			W_histogram_.clear();
126	gezelter	1054	for (int l = 0; l <= lMax_; l++) {
127			for (int m = -l; m <= l; m++) {
128			w3j[std::make_pair(l,m)].clear();
129			}
130			}
131			w3j.clear();
132			m2Min.clear();
133			m2Max.clear();
134	gezelter	1041	}
135	gezelter	1054
136	gezelter	1048	void BondOrderParameter::initalizeHistogram() {
137	gezelter	1051	for (int bin = 0; bin < nBins_; bin++) {
138			for (int l = 0; l <= lMax_; l++) {
139			Q_histogram_[std::make_pair(bin,l)] = 0;
140			W_histogram_[std::make_pair(bin,l)] = 0;
141			}
142			}
143	gezelter	1048	}
144
145	gezelter	1039	void BondOrderParameter::process() {
146			Molecule* mol;
147			Atom* atom;
148			RigidBody* rb;
149	gezelter	1043	int myIndex;
150	gezelter	1039	SimInfo::MoleculeIterator mi;
151			Molecule::RigidBodyIterator rbIter;
152			Molecule::AtomIterator ai;
153			StuntDouble* sd;
154	gezelter	1043	Vector3d vec;
155	gezelter	1042	RealType costheta;
156	gezelter	1039	RealType phi;
157			RealType r;
158			RealType dist;
159	gezelter	1051	std::map<std::pair<int,int>,ComplexType> q;
160			std::vector<RealType> q_l;
161	gezelter	1052	std::vector<RealType> q2;
162			std::vector<ComplexType> w;
163			std::vector<ComplexType> w_hat;
164	gezelter	1051	std::map<std::pair<int,int>,ComplexType> QBar;
165			std::vector<RealType> Q2;
166			std::vector<RealType> Q;
167			std::vector<ComplexType> W;
168			std::vector<ComplexType> W_hat;
169	gezelter	1048	int nBonds, Nbonds;
170	gezelter	1042	SphericalHarmonic sphericalHarmonic;
171	gezelter	1039	int i, j;
172	gezelter	1043
173	gezelter	1039	DumpReader reader(info_, dumpFilename_);
174			int nFrames = reader.getNFrames();
175	gezelter	1041	frameCounter_ = 0;
176	chuckv	1038
177	gezelter	1051	q_l.resize(lMax_+1);
178	gezelter	1052	q2.resize(lMax_+1);
179			w.resize(lMax_+1);
180			w_hat.resize(lMax_+1);
181
182	gezelter	1051	Q2.resize(lMax_+1);
183			Q.resize(lMax_+1);
184			W.resize(lMax_+1);
185			W_hat.resize(lMax_+1);
186	gezelter	1094	Nbonds = 0;
187	gezelter	1051
188	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
189			reader.readFrame(istep);
190	gezelter	1041	frameCounter_++;
191	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
192
193			if (evaluator_.isDynamic()) {
194			seleMan_.setSelectionSet(evaluator_.evaluate());
195			}
196	chuckv	1038
197	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
198	chuckv	1038
199	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
200			mol = info_->nextMolecule(mi)) {
201			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
202			rb = mol->nextRigidBody(rbIter)) {
203			rb->updateAtoms();
204			}
205	gezelter	1048	}
206
207	gezelter	1039	// outer loop is over the selected StuntDoubles:
208	chuckv	1038
209	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
210			sd = seleMan_.nextSelected(i)) {
211	chuckv	1038
212	gezelter	1043	myIndex = sd->getGlobalIndex();
213	gezelter	1048	nBonds = 0;
214	gezelter	1051
215			for (int l = 0; l <= lMax_; l++) {
216			for (int m = -l; m <= l; m++) {
217			q[std::make_pair(l,m)] = 0.0;
218			}
219	gezelter	1048	}
220	gezelter	1039
221			// inner loop is over all other atoms in the system:
222
223			for (mol = info_->beginMolecule(mi); mol != NULL;
224			mol = info_->nextMolecule(mi)) {
225			for (atom = mol->beginAtom(ai); atom != NULL;
226			atom = mol->nextAtom(ai)) {
227	chuckv	1038
228	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
229	chuckv	1038
230	gezelter	1043	vec = sd->getPos() - atom->getPos();
231	gezelter	1078
232			if (usePeriodicBoundaryConditions_)
233			currentSnapshot_->wrapVector(vec);
234	gezelter	1042
235	gezelter	1043	// 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	1051
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	1043	}
255			nBonds++;
256			}
257			}
258	gezelter	1039	}
259			}
260	gezelter	1051
261
262	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
263			q2[l] = 0.0;
264			for (int m = -l; m <= l; m++){
265	gezelter	1094	q[std::make_pair(l,m)] /= (RealType)nBonds;
266	gezelter	1052	q2[l] += norm(q[std::make_pair(l,m)]);
267			}
268	gezelter	1094	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
269	gezelter	1052	}
270	gezelter	1094
271	gezelter	1052	// 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	1053	std::pair<int,int> lm = std::make_pair(l, m1);
277	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
278	gezelter	1053	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	1052	}
283			}
284
285			w_hat[l] = w[l] / pow(q2[l], 1.5);
286			}
287
288			collectHistogram(q_l, w_hat);
289
290	gezelter	1048	Nbonds += nBonds;
291	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
292			for (int m = -l; m <= l; m++) {
293	gezelter	1094	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
294	gezelter	1051	}
295	gezelter	1048	}
296			}
297	gezelter	1047	}
298	gezelter	1051
299	gezelter	1047	// Normalize Qbar2
300	gezelter	1051	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	1039	}
305
306	gezelter	1047	// Find second order invariant Q_l
307	gezelter	1039
308	gezelter	1051	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	1039	}
315	gezelter	1047
316			// Find Third Order Invariant W_l
317
318	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
319			W[l] = 0.0;
320			for (int m1 = -l; m1 <= l; m1++) {
321	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
322	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
323	gezelter	1053	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	1051	}
328	gezelter	1047	}
329	gezelter	1041
330	gezelter	1051	W_hat[l] = W[l] / pow(Q2[l], 1.5);
331	gezelter	1039	}
332	gezelter	1047
333	gezelter	1051	writeOrderParameter(Q, W_hat);
334	gezelter	1047	}
335	chuckv	1038
336	gezelter	1052	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337			std::vector<ComplexType> what) {
338	chuckv	1038
339	gezelter	1051	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
348	gezelter	1051	painCave.isFatal = 1;
349			simError();
350			}
351	gezelter	1048	}
352
353	gezelter	1052	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	gezelter	1094	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
361	gezelter	1390	painCave.severity = OPENMD_ERROR;
362	gezelter	1052	painCave.isFatal = 1;
363			simError();
364			}
365			}
366
367	gezelter	1048	}
368
369
370	gezelter	1052	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371			std::vector<ComplexType> What) {
372	gezelter	1051
373	gezelter	1052	std::ofstream osq((getOutputFileName() + "q").c_str());
374
375			if (osq.is_open()) {
376	gezelter	1041
377	gezelter	1052	osq << "# Bond Order Parameters\n";
378			osq << "# selection: (" << selectionScript_ << ")\n";
379			osq << "# \n";
380	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
381	gezelter	1052	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
382	gezelter	1051	}
383	gezelter	1048	// Normalize by number of frames and write it out:
384	gezelter	1051	for (int i = 0; i < nBins_; ++i) {
385			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386	gezelter	1052	osq << Qval;
387	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
388	gezelter	1094
389			osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
390	gezelter	1051	}
391	gezelter	1052	osq << "\n";
392	gezelter	1048	}
393
394	gezelter	1052	osq.close();
395	gezelter	1047
396	gezelter	1041	} else {
397			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
398	gezelter	1052	(getOutputFileName() + "q").c_str());
399	gezelter	1041	painCave.isFatal = 1;
400			simError();
401			}
402	gezelter	1052
403			std::ofstream osw((getOutputFileName() + "w").c_str());
404
405			if (osw.is_open()) {
406			osw << "# Bond Order Parameters\n";
407			osw << "# selection: (" << selectionScript_ << ")\n";
408			osw << "# \n";
409			for (int l = 0; l <= lMax_; l++) {
410	gezelter	1090	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
411	gezelter	1052	}
412			// Normalize by number of frames and write it out:
413			for (int i = 0; i < nBins_; ++i) {
414			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
415			osw << Wval;
416			for (int l = 0; l <= lMax_; l++) {
417	gezelter	1094
418			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
419	gezelter	1052	}
420			osw << "\n";
421			}
422
423			osw.close();
424			} else {
425			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
426			(getOutputFileName() + "w").c_str());
427			painCave.isFatal = 1;
428			simError();
429			}
430
431	gezelter	1041	}
432	gezelter	1039	}