applications/staticProps/BondOrderParameter.cpp

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


/* Creates orientational bond order parameters as outlined by
 *     Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
 *     Phys Rev B, 28,784,1983
 * 
 */
 
#include "applications/staticProps/BondOrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

namespace oopse {

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

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

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

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

    // Q can take values from 0 to 1

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

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

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

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

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

  void BondOrderParameter::process() {
    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator ai;
    StuntDouble* sd;
    Vector3d vec;
    RealType costheta;
    RealType phi;
    RealType r;
    RealType dist;
    std::map<std::pair<int,int>,ComplexType> q;
    std::vector<RealType> q_l;
    std::vector<RealType> q2;
    std::vector<ComplexType> w;
    std::vector<ComplexType> w_hat;
    std::map<std::pair<int,int>,ComplexType> QBar;
    std::vector<RealType> Q2;
    std::vector<RealType> Q;
    std::vector<ComplexType> W;
    std::vector<ComplexType> W_hat;
    int nBonds, Nbonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;
    // Make arrays for Wigner3jm
    double* THRCOF = new double[2*lMax_+1];
    // Variables for Wigner routine
    double lPass, m1Pass, m2Min, m2Max;
    int error, m1, m2, m3, mSize;
    mSize = 2*lMax_+1;

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

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

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

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

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

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

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

        myIndex = sd->getGlobalIndex();
        nBonds = 0;
        
        for (int l = 0; l <= lMax_; l++) {
          for (int m = -l; m <= l; m++) {
            q[std::make_pair(l,m)] = 0.0;
          }
        }
        
        // inner loop is over all other atoms in the system:
        
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          for (atom = mol->beginAtom(ai); atom != NULL; 
               atom = mol->nextAtom(ai)) {

            if (atom->getGlobalIndex() != myIndex) {

              vec = sd->getPos() - atom->getPos();       
              currentSnapshot_->wrapVector(vec);
              
              // Calculate "bonds" and build Q_lm(r) where 
              //      Q_lm = Y_lm(theta(r),phi(r))                
              // The spherical harmonics are wrt any arbitrary coordinate
              // system, we choose standard spherical coordinates 
              
              r = vec.length();
              
              // Check to see if neighbor is in bond cutoff 
              
              if (r < rCut_) { 
                costheta = vec.z() / r; 
                phi = atan2(vec.y(), vec.x());

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

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

        // Find Third Order Invariant W_l
    
        for (int l = 0; l <= lMax_; l++) {
          w[l] = 0.0;
          lPass = (double)l;
          for (int m1 = -l; m1 <= l; m1++) {
            // Zero work array
            for (int ii = 0; ii < 2*l + 1; ii++){
              THRCOF[ii] = 0.0;
            }
            // Get Wigner coefficients
            m1Pass = (double)m1;
            
            Wigner3jm(&lPass, &lPass, &lPass, 
                      &m1Pass, &m2Min, &m2Max, 
                      THRCOF, &mSize, &error);
            
            for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
              m2 = (int)floor(m2Min) + mmm;
              m3 = -m1-m2;
              w[l] += THRCOF[mmm] * 
                q[std::make_pair(l,m1)] * 
                q[std::make_pair(l,m2)] * 
                q[std::make_pair(l,m3)];
            }
          }
          
          w_hat[l] = w[l] / pow(q2[l], 1.5);
        }

        collectHistogram(q_l, w_hat);
        
        Nbonds += nBonds;
        for (int l = 0; l <= lMax_;  l++) {
          for (int m = -l; m <= l; m++) {
            QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
          }
        }
      }
    }
      
    // Normalize Qbar2
    for (int l = 0; l <= lMax_; l++) {
      for (int m = -l; m <= l; m++){
        QBar[std::make_pair(l,m)] /= Nbonds;
      }
    }
    
    // Find second order invariant Q_l
    
    for (int l = 0; l <= lMax_; l++) {
      Q2[l] = 0.0;
      for (int m = -l; m <= l; m++){
        Q2[l] += norm(QBar[std::make_pair(l,m)]);
      }
      Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
    }
    
    // Find Third Order Invariant W_l
    
    for (int l = 0; l <= lMax_; l++) {
      W[l] = 0.0;
      lPass = (double)l;
      for (int m1 = -l; m1 <= l; m1++) {
        // Zero work array
        for (int ii = 0; ii < 2*l + 1; ii++){
          THRCOF[ii] = 0.0;
        }
        // Get Wigner coefficients
        m1Pass = (double)m1;
        
        Wigner3jm(&lPass, &lPass, &lPass, 
                  &m1Pass, &m2Min, &m2Max, 
                  THRCOF, &mSize, &error);
        
        for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
          m2 = (int)floor(m2Min) + mmm;
          m3 = -m1-m2;
          W[l] += THRCOF[mmm] * 
            QBar[std::make_pair(l,m1)] * 
            QBar[std::make_pair(l,m2)] * 
            QBar[std::make_pair(l,m3)];
        }
      }
      
      W_hat[l] = W[l] / pow(Q2[l], 1.5);
    }
    
    writeOrderParameter(Q, W_hat);    
  }

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

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

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

  }  


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

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

      osq.close();

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

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

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

      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
       
  }
}
Revision:	3022
Committed:	Tue Sep 26 01:30:32 2006 UTC (17 years, 9 months ago) by gezelter
File size:	13820 byte(s)
Log Message:	Mostly done with BondOrderParameter. Only a few performance tweaks remain
#	Content
1	/*
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
49	#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
55	namespace oopse {
56
57	BondOrderParameter::BondOrderParameter(SimInfo* info,
58	const std::string& filename,
59	const std::string& sele,
60	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61
62	setOutputName(getPrefix(filename) + ".bo");
63
64	evaluator_.loadScriptString(sele);
65	if (!evaluator_.isDynamic()) {
66	seleMan_.setSelectionSet(evaluator_.evaluate());
67	}
68
69	// Set up cutoff radius and order of the Legendre Polynomial:
70
71	rCut_ = rCut;
72	nBins_ = nbins;
73	Qcount_.resize(lMax_+1);
74	Wcount_.resize(lMax_+1);
75
76	// Q can take values from 0 to 1
77
78	MinQ_ = 0.0;
79	MaxQ_ = 1.1;
80	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	MinW_ = -0.25;
86	MaxW_ = 0.25;
87	deltaW_ = (MaxW_ - MinW_) / nbins;
88	}
89
90	BondOrderParameter::~BondOrderParameter() {
91	Q_histogram_.clear();
92	W_histogram_.clear();
93	}
94
95	void BondOrderParameter::initalizeHistogram() {
96	for (int bin = 0; bin < nBins_; bin++) {
97	for (int l = 0; l <= lMax_; l++) {
98	Q_histogram_[std::make_pair(bin,l)] = 0;
99	W_histogram_[std::make_pair(bin,l)] = 0;
100	}
101	}
102	}
103
104	void BondOrderParameter::process() {
105	Molecule* mol;
106	Atom* atom;
107	RigidBody* rb;
108	int myIndex;
109	SimInfo::MoleculeIterator mi;
110	Molecule::RigidBodyIterator rbIter;
111	Molecule::AtomIterator ai;
112	StuntDouble* sd;
113	Vector3d vec;
114	RealType costheta;
115	RealType phi;
116	RealType r;
117	RealType dist;
118	std::map<std::pair<int,int>,ComplexType> q;
119	std::vector<RealType> q_l;
120	std::vector<RealType> q2;
121	std::vector<ComplexType> w;
122	std::vector<ComplexType> w_hat;
123	std::map<std::pair<int,int>,ComplexType> QBar;
124	std::vector<RealType> Q2;
125	std::vector<RealType> Q;
126	std::vector<ComplexType> W;
127	std::vector<ComplexType> W_hat;
128	int nBonds, Nbonds;
129	SphericalHarmonic sphericalHarmonic;
130	int i, j;
131	// Make arrays for Wigner3jm
132	double* THRCOF = new double[2*lMax_+1];
133	// Variables for Wigner routine
134	double lPass, m1Pass, m2Min, m2Max;
135	int error, m1, m2, m3, mSize;
136	mSize = 2*lMax_+1;
137
138	DumpReader reader(info_, dumpFilename_);
139	int nFrames = reader.getNFrames();
140	frameCounter_ = 0;
141
142	q_l.resize(lMax_+1);
143	q2.resize(lMax_+1);
144	w.resize(lMax_+1);
145	w_hat.resize(lMax_+1);
146
147	Q2.resize(lMax_+1);
148	Q.resize(lMax_+1);
149	W.resize(lMax_+1);
150	W_hat.resize(lMax_+1);
151
152	for (int istep = 0; istep < nFrames; istep += step_) {
153	reader.readFrame(istep);
154	frameCounter_++;
155	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
156
157	if (evaluator_.isDynamic()) {
158	seleMan_.setSelectionSet(evaluator_.evaluate());
159	}
160
161	// update the positions of atoms which belong to the rigidbodies
162
163	for (mol = info_->beginMolecule(mi); mol != NULL;
164	mol = info_->nextMolecule(mi)) {
165	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
166	rb = mol->nextRigidBody(rbIter)) {
167	rb->updateAtoms();
168	}
169	}
170
171	// outer loop is over the selected StuntDoubles:
172
173	for (sd = seleMan_.beginSelected(i); sd != NULL;
174	sd = seleMan_.nextSelected(i)) {
175
176	myIndex = sd->getGlobalIndex();
177	nBonds = 0;
178
179	for (int l = 0; l <= lMax_; l++) {
180	for (int m = -l; m <= l; m++) {
181	q[std::make_pair(l,m)] = 0.0;
182	}
183	}
184
185	// inner loop is over all other atoms in the system:
186
187	for (mol = info_->beginMolecule(mi); mol != NULL;
188	mol = info_->nextMolecule(mi)) {
189	for (atom = mol->beginAtom(ai); atom != NULL;
190	atom = mol->nextAtom(ai)) {
191
192	if (atom->getGlobalIndex() != myIndex) {
193
194	vec = sd->getPos() - atom->getPos();
195	currentSnapshot_->wrapVector(vec);
196
197	// Calculate "bonds" and build Q_lm(r) where
198	// Q_lm = Y_lm(theta(r),phi(r))
199	// The spherical harmonics are wrt any arbitrary coordinate
200	// system, we choose standard spherical coordinates
201
202	r = vec.length();
203
204	// Check to see if neighbor is in bond cutoff
205
206	if (r < rCut_) {
207	costheta = vec.z() / r;
208	phi = atan2(vec.y(), vec.x());
209
210	for (int l = 0; l <= lMax_; l++) {
211	sphericalHarmonic.setL(l);
212	for(int m = -l; m <= l; m++){
213	sphericalHarmonic.setM(m);
214	q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
215	}
216	}
217	nBonds++;
218	}
219	}
220	}
221	}
222
223
224	for (int l = 0; l <= lMax_; l++) {
225	q_l[l] = 0.0;
226	for(int m = -l; m <= l; m++) {
227	q_l[l] += norm(q[std::make_pair(l,m)]);
228	}
229	q_l[l] = 4.0NumericConstant::PI/(RealType)(2*l + 1);
230	q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231	}
232
233	// Find second order invariant Q_l
234
235	for (int l = 0; l <= lMax_; l++) {
236	q2[l] = 0.0;
237	for (int m = -l; m <= l; m++){
238	q2[l] += norm(q[std::make_pair(l,m)]);
239	}
240	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241	(RealType)(2*l + 1))/(RealType)nBonds;
242	}
243
244	// Find Third Order Invariant W_l
245
246	for (int l = 0; l <= lMax_; l++) {
247	w[l] = 0.0;
248	lPass = (double)l;
249	for (int m1 = -l; m1 <= l; m1++) {
250	// Zero work array
251	for (int ii = 0; ii < 2*l + 1; ii++){
252	THRCOF[ii] = 0.0;
253	}
254	// Get Wigner coefficients
255	m1Pass = (double)m1;
256
257	Wigner3jm(&lPass, &lPass, &lPass,
258	&m1Pass, &m2Min, &m2Max,
259	THRCOF, &mSize, &error);
260
261	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
262	m2 = (int)floor(m2Min) + mmm;
263	m3 = -m1-m2;
264	w[l] += THRCOF[mmm] *
265	q[std::make_pair(l,m1)] *
266	q[std::make_pair(l,m2)] *
267	q[std::make_pair(l,m3)];
268	}
269	}
270
271	w_hat[l] = w[l] / pow(q2[l], 1.5);
272	}
273
274	collectHistogram(q_l, w_hat);
275
276	Nbonds += nBonds;
277	for (int l = 0; l <= lMax_; l++) {
278	for (int m = -l; m <= l; m++) {
279	QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
280	}
281	}
282	}
283	}
284
285	// Normalize Qbar2
286	for (int l = 0; l <= lMax_; l++) {
287	for (int m = -l; m <= l; m++){
288	QBar[std::make_pair(l,m)] /= Nbonds;
289	}
290	}
291
292	// Find second order invariant Q_l
293
294	for (int l = 0; l <= lMax_; l++) {
295	Q2[l] = 0.0;
296	for (int m = -l; m <= l; m++){
297	Q2[l] += norm(QBar[std::make_pair(l,m)]);
298	}
299	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
300	}
301
302	// Find Third Order Invariant W_l
303
304	for (int l = 0; l <= lMax_; l++) {
305	W[l] = 0.0;
306	lPass = (double)l;
307	for (int m1 = -l; m1 <= l; m1++) {
308	// Zero work array
309	for (int ii = 0; ii < 2*l + 1; ii++){
310	THRCOF[ii] = 0.0;
311	}
312	// Get Wigner coefficients
313	m1Pass = (double)m1;
314
315	Wigner3jm(&lPass, &lPass, &lPass,
316	&m1Pass, &m2Min, &m2Max,
317	THRCOF, &mSize, &error);
318
319	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
320	m2 = (int)floor(m2Min) + mmm;
321	m3 = -m1-m2;
322	W[l] += THRCOF[mmm] *
323	QBar[std::make_pair(l,m1)] *
324	QBar[std::make_pair(l,m2)] *
325	QBar[std::make_pair(l,m3)];
326	}
327	}
328
329	W_hat[l] = W[l] / pow(Q2[l], 1.5);
330	}
331
332	writeOrderParameter(Q, W_hat);
333	}
334
335	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
336	std::vector<ComplexType> what) {
337
338	for (int l = 0; l <= lMax_; l++) {
339	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
340	int qbin = (q[l] - MinQ_) / deltaQ_;
341	Q_histogram_[std::make_pair(qbin,l)] += 1;
342	Qcount_[l]++;
343	} else {
344	sprintf( painCave.errMsg,
345	"q_l value outside reasonable range\n");
346	painCave.severity = OOPSE_ERROR;
347	painCave.isFatal = 1;
348	simError();
349	}
350	}
351
352	for (int l = 0; l <= lMax_; l++) {
353	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
354	int wbin = (real(what[l]) - MinW_) / deltaW_;
355	W_histogram_[std::make_pair(wbin,l)] += 1;
356	Wcount_[l]++;
357	} else {
358	sprintf( painCave.errMsg,
359	"Re[w_hat] value outside reasonable range\n");
360	painCave.severity = OOPSE_ERROR;
361	painCave.isFatal = 1;
362	simError();
363	}
364	}
365
366	}
367
368
369	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
370	std::vector<ComplexType> What) {
371
372	std::ofstream osq((getOutputFileName() + "q").c_str());
373
374	if (osq.is_open()) {
375
376	osq << "# Bond Order Parameters\n";
377	osq << "# selection: (" << selectionScript_ << ")\n";
378	osq << "# \n";
379	for (int l = 0; l <= lMax_; l++) {
380	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
381	}
382	// Normalize by number of frames and write it out:
383	for (int i = 0; i < nBins_; ++i) {
384	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
385	osq << Qval;
386	for (int l = 0; l <= lMax_; l++) {
387	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
388	}
389	osq << "\n";
390	}
391
392	osq.close();
393
394	} else {
395	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
396	(getOutputFileName() + "q").c_str());
397	painCave.isFatal = 1;
398	simError();
399	}
400
401	std::ofstream osw((getOutputFileName() + "w").c_str());
402
403	if (osw.is_open()) {
404	osw << "# Bond Order Parameters\n";
405	osw << "# selection: (" << selectionScript_ << ")\n";
406	osw << "# \n";
407	for (int l = 0; l <= lMax_; l++) {
408	osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
409	}
410	// Normalize by number of frames and write it out:
411	for (int i = 0; i < nBins_; ++i) {
412	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
413	osw << Wval;
414	for (int l = 0; l <= lMax_; l++) {
415	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
416	}
417	osw << "\n";
418	}
419
420	osw.close();
421	} else {
422	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
423	(getOutputFileName() + "w").c_str());
424	painCave.isFatal = 1;
425	simError();
426	}
427
428	}
429	}