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"
#include "math/SphericalHarmonic.hpp"

namespace oopse {

  BondOrderParameter::BondOrderParameter(SimInfo* info, 
                                         const std::string& filename, 
                                         const std::string& sele,
                                         double rCut, int lNumber, 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:

    lNumber_ = lNumber;
    rCut_ = rCut;
    mSize_ = 2*lNumber_+1;    

    // Q can take values from 0 to 1

    MinQ_ = 0.0;
    MaxQ_ = 1.0;
    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
    Q_histogram_.resize(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_ = -0.18;
    MaxW_ = 0.18;
    deltaW_ = (MaxW_ - MinW_) / nbins;
    W_histogram_.resize(nbins);

  }

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

  void BondOrderParameter::initalizeHistogram() {
    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
    std::fill(W_histogram_.begin(), W_histogram_.end(), 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<int, ComplexType> QBar_lm;
    RealType QSq_l;
    RealType Q_l;
    ComplexType W_l;
    ComplexType W_l_hat;
    int nBonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;
    // Make arrays for Wigner3jm
    double* THRCOF = new double[mSize_];
    // Variables for Wigner routine
    double l_ = (double)lNumber_;
    double m1Pass, m2Min, m2Max;
    int error, m1, m2, m3;

    // Set the l for the spherical harmonic, it doesn't change
    sphericalHarmonic.setL(lNumber_);

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

        // For this central atom, zero out nBonds and QBar_lm

        nBonds = 0;
       
        for (int m = -lNumber_; m <= lNumber_; m++) {
          QBar_lm[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 m = -lNumber_; m <= lNumber_; m++){
                  sphericalHarmonic.setM(m);
                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
                }
                nBonds++;
              }  
            }
          }
        }
        
        // Normalize Qbar2
        for (int m = -lNumber_;m <= lNumber_; m++){
          QBar_lm[m] /= nBonds; 
          std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
        }

        // Find second order invariant Q_l

        QSq_l = 0.0;
        for (int m = -lNumber_; m <= lNumber_; m++){
          QSq_l += norm(QBar_lm[m]);
        }
        std::cout << "qsq_l = " << QSq_l << "\n";
        Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / 
                   (2.0*(RealType)lNumber_ + 1.0));

        // Find Third Order Invariant W_l
        
        W_l = 0.0;
        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
          // Zero work array
          for (int ii = 0; ii < mSize_; ii++){
            THRCOF[i] = 0.0;
          }
          // Get Wigner coefficients
          m1Pass = (double)m1;
          Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
          for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
            m2 = floor(m2Min) + m_index - 1;
            m3 = -m1-m2;
            W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3];
          }
        }
        
        W_l_hat = W_l / pow(QSq_l, 1.5);
        
        // accumulate histogram data for Q_l and W_l_hat:

        std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
        collectHistogram(Q_l, real(W_l_hat));
                
      }
    }
    
    writeOrderParameter();
    
  }


  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {

    if (Q_l >= MinQ_ && Q_l < MaxQ_) {
      int qbin = (Q_l - MinQ_) / deltaQ_;
      Q_histogram_[qbin] += 1;
      Qcount_++;
      sumQ_ += Q_l;
      sumQ2_ += Q_l * Q_l;
    } else {
      sprintf( painCave.errMsg,
               "Q_l value outside reasonable range\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();  
    }

    if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
      int wbin = (W_l_hat - MinW_) / deltaW_;
      W_histogram_[wbin] += 1;
      Wcount_++;
      sumW_  += W_l_hat;
      sumW2_ += W_l_hat*W_l_hat;
    } else {
      sprintf( painCave.errMsg,
               "W_l_hat value outside reasonable range\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  }  

  void BondOrderParameter::writeOrderParameter() {

    std::ofstream osq((getOutputFileName() + "q").c_str());

    if (osq.is_open()) {

      RealType qAvg = sumQ_ / (RealType) Qcount_;
      RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
      
      osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
      osq << "# selection: (" << selectionScript_ << ")\n";
      osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
      osq << "# std. dev.: " << qStdDev << "\n";
      
      // Normalize by number of frames and write it out:
      for (int i = 0; i < Q_histogram_.size(); ++i) {
        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
        osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\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()) {

      RealType wAvg = sumW_ / (RealType) Wcount_;
      RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
      
      osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
      osw << "# selection: (" << selectionScript_ << ")\n";
      osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
      osw << "# std. dev.: " << wStdDev << "\n";
      
      // Normalize by number of frames and write it out:
      for (int i = 0; i < W_histogram_.size(); ++i) {
        RealType Wval = MinW_ + (i + 0.5) * deltaW_;
        osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
      }
      
      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
  }
}
Revision:	3012
Committed:	Thu Sep 21 18:04:52 2006 UTC (17 years, 9 months ago) by gezelter
File size:	11356 byte(s)
Log Message:	Fixed a bug in Wl code in BondOrderParameter
#	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	#include "math/SphericalHarmonic.hpp"
55
56	namespace oopse {
57
58	BondOrderParameter::BondOrderParameter(SimInfo* info,
59	const std::string& filename,
60	const std::string& sele,
61	double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62
63	setOutputName(getPrefix(filename) + ".bo");
64
65	evaluator_.loadScriptString(sele);
66	if (!evaluator_.isDynamic()) {
67	seleMan_.setSelectionSet(evaluator_.evaluate());
68	}
69
70	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	lNumber_ = lNumber;
73	rCut_ = rCut;
74	mSize_ = 2*lNumber_+1;
75
76	// Q can take values from 0 to 1
77
78	MinQ_ = 0.0;
79	MaxQ_ = 1.0;
80	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81	Q_histogram_.resize(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	MinW_ = -0.18;
87	MaxW_ = 0.18;
88	deltaW_ = (MaxW_ - MinW_) / nbins;
89	W_histogram_.resize(nbins);
90
91	}
92
93	BondOrderParameter::~BondOrderParameter() {
94	Q_histogram_.clear();
95	W_histogram_.clear();
96	}
97
98	void BondOrderParameter::initalizeHistogram() {
99	std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
100	std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
101	}
102
103	void BondOrderParameter::process() {
104	Molecule* mol;
105	Atom* atom;
106	RigidBody* rb;
107	int myIndex;
108	SimInfo::MoleculeIterator mi;
109	Molecule::RigidBodyIterator rbIter;
110	Molecule::AtomIterator ai;
111	StuntDouble* sd;
112	Vector3d vec;
113	RealType costheta;
114	RealType phi;
115	RealType r;
116	RealType dist;
117	std::map<int, ComplexType> QBar_lm;
118	RealType QSq_l;
119	RealType Q_l;
120	ComplexType W_l;
121	ComplexType W_l_hat;
122	int nBonds;
123	SphericalHarmonic sphericalHarmonic;
124	int i, j;
125	// Make arrays for Wigner3jm
126	double* THRCOF = new double[mSize_];
127	// Variables for Wigner routine
128	double l_ = (double)lNumber_;
129	double m1Pass, m2Min, m2Max;
130	int error, m1, m2, m3;
131
132	// Set the l for the spherical harmonic, it doesn't change
133	sphericalHarmonic.setL(lNumber_);
134
135	DumpReader reader(info_, dumpFilename_);
136	int nFrames = reader.getNFrames();
137	frameCounter_ = 0;
138
139	for (int istep = 0; istep < nFrames; istep += step_) {
140	reader.readFrame(istep);
141	frameCounter_++;
142	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
143
144	if (evaluator_.isDynamic()) {
145	seleMan_.setSelectionSet(evaluator_.evaluate());
146	}
147
148	// update the positions of atoms which belong to the rigidbodies
149
150	for (mol = info_->beginMolecule(mi); mol != NULL;
151	mol = info_->nextMolecule(mi)) {
152	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
153	rb = mol->nextRigidBody(rbIter)) {
154	rb->updateAtoms();
155	}
156	}
157
158	// outer loop is over the selected StuntDoubles:
159
160	for (sd = seleMan_.beginSelected(i); sd != NULL;
161	sd = seleMan_.nextSelected(i)) {
162
163	myIndex = sd->getGlobalIndex();
164
165	// For this central atom, zero out nBonds and QBar_lm
166
167	nBonds = 0;
168
169	for (int m = -lNumber_; m <= lNumber_; m++) {
170	QBar_lm[m] = 0.0;
171	}
172
173	// inner loop is over all other atoms in the system:
174
175	for (mol = info_->beginMolecule(mi); mol != NULL;
176	mol = info_->nextMolecule(mi)) {
177	for (atom = mol->beginAtom(ai); atom != NULL;
178	atom = mol->nextAtom(ai)) {
179
180	if (atom->getGlobalIndex() != myIndex) {
181
182	vec = sd->getPos() - atom->getPos();
183	currentSnapshot_->wrapVector(vec);
184
185	// Calculate "bonds" and build Q_lm(r) where
186	// Q_lm = Y_lm(theta(r),phi(r))
187	// The spherical harmonics are wrt any arbitrary coordinate
188	// system, we choose standard spherical coordinates
189
190	r = vec.length();
191
192	// Check to see if neighbor is in bond cutoff
193
194	if (r < rCut_) {
195	costheta = vec.z() / r;
196	phi = atan2(vec.y(), vec.x());
197
198	for(int m = -lNumber_; m <= lNumber_; m++){
199	sphericalHarmonic.setM(m);
200	QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
201	}
202	nBonds++;
203	}
204	}
205	}
206	}
207
208	// Normalize Qbar2
209	for (int m = -lNumber_;m <= lNumber_; m++){
210	QBar_lm[m] /= nBonds;
211	std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
212	}
213
214	// Find second order invariant Q_l
215
216	QSq_l = 0.0;
217	for (int m = -lNumber_; m <= lNumber_; m++){
218	QSq_l += norm(QBar_lm[m]);
219	}
220	std::cout << "qsq_l = " << QSq_l << "\n";
221	Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
222	(2.0*(RealType)lNumber_ + 1.0));
223
224	// Find Third Order Invariant W_l
225
226	W_l = 0.0;
227	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
228	// Zero work array
229	for (int ii = 0; ii < mSize_; ii++){
230	THRCOF[i] = 0.0;
231	}
232	// Get Wigner coefficients
233	m1Pass = (double)m1;
234	Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
235	for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
236	m2 = floor(m2Min) + m_index - 1;
237	m3 = -m1-m2;
238	W_l += THRCOF[m_index]QBar_lm[m1]QBar_lm[m2]*QBar_lm[m3];
239	}
240	}
241
242	W_l_hat = W_l / pow(QSq_l, 1.5);
243
244	// accumulate histogram data for Q_l and W_l_hat:
245
246	std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
247	collectHistogram(Q_l, real(W_l_hat));
248
249	}
250	}
251
252	writeOrderParameter();
253
254	}
255
256
257	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
258
259	if (Q_l >= MinQ_ && Q_l < MaxQ_) {
260	int qbin = (Q_l - MinQ_) / deltaQ_;
261	Q_histogram_[qbin] += 1;
262	Qcount_++;
263	sumQ_ += Q_l;
264	sumQ2_ += Q_l * Q_l;
265	} else {
266	sprintf( painCave.errMsg,
267	"Q_l value outside reasonable range\n");
268	painCave.severity = OOPSE_ERROR;
269	painCave.isFatal = 1;
270	simError();
271	}
272
273	if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
274	int wbin = (W_l_hat - MinW_) / deltaW_;
275	W_histogram_[wbin] += 1;
276	Wcount_++;
277	sumW_ += W_l_hat;
278	sumW2_ += W_l_hat*W_l_hat;
279	} else {
280	sprintf( painCave.errMsg,
281	"W_l_hat value outside reasonable range\n");
282	painCave.severity = OOPSE_ERROR;
283	painCave.isFatal = 1;
284	simError();
285	}
286	}
287
288	void BondOrderParameter::writeOrderParameter() {
289
290	std::ofstream osq((getOutputFileName() + "q").c_str());
291
292	if (osq.is_open()) {
293
294	RealType qAvg = sumQ_ / (RealType) Qcount_;
295	RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
296
297	osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
298	osq << "# selection: (" << selectionScript_ << ")\n";
299	osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
300	osq << "# std. dev.: " << qStdDev << "\n";
301
302	// Normalize by number of frames and write it out:
303	for (int i = 0; i < Q_histogram_.size(); ++i) {
304	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
305	osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
306	}
307
308	osq.close();
309	} else {
310	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
311	(getOutputFileName() + "q").c_str());
312	painCave.isFatal = 1;
313	simError();
314	}
315
316	std::ofstream osw((getOutputFileName() + "w").c_str());
317
318	if (osw.is_open()) {
319
320	RealType wAvg = sumW_ / (RealType) Wcount_;
321	RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
322
323	osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
324	osw << "# selection: (" << selectionScript_ << ")\n";
325	osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
326	osw << "# std. dev.: " << wStdDev << "\n";
327
328	// Normalize by number of frames and write it out:
329	for (int i = 0; i < W_histogram_.size(); ++i) {
330	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
331	osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
332	}
333
334	osw.close();
335	} else {
336	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
337	(getOutputFileName() + "w").c_str());
338	painCave.isFatal = 1;
339	simError();
340	}
341	}
342	}