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;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator ai;
    StuntDouble* sd;
    RealType costheta;
    RealType phi;
    RealType r;
    RealType dist;
    std::map<int, ComplexType> QBar_lm;
    RealType QSq_l;
    RealType Q_l;
    int nBonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;
  
    // 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)) {

        // 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)) {


            Vector3d 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 = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
            
            // 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; 
        }

        // Find second order invariant Q_l

        QSq_l = 0.0;
        for (int m = -lNumber_; m <= lNumber_; m++){
          QSq_l += norm(QBar_lm[m]);
        }
        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
     
        // Find Third Order Invariant W_l

        // 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;

        ComplexType W_l;
        ComplexType W_l_hat;
        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; i < (int)(m2Max - m2Min-1.0); m_index++) {
            m2 = floor(m2Min) + m_index - 1;
            m3 = -m1-m2;
            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
          }
        }

        W_l_hat = W_l / pow(QSq_l, 1.5);

        // accumulate histogram data for Q_l and W_l_hat:

        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:	3010
Committed:	Wed Sep 20 22:16:23 2006 UTC (17 years, 9 months ago) by gezelter
File size:	11044 byte(s)
Log Message:	added SphericalHarmonics, fixed a few problems with BondOrderParameter
#	User	Rev	Content
1	chuckv	3005	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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	gezelter	3007
49	chuckv	3005	#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	gezelter	3010	#include "math/SphericalHarmonic.hpp"
55	gezelter	3009
56	chuckv	3005	namespace oopse {
57
58	gezelter	3007	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	3009	double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	3007
63	gezelter	3009	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	3005
65	gezelter	3007	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	3005	}
69
70	gezelter	3007	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	3005	lNumber_ = lNumber;
73			rCut_ = rCut;
74	gezelter	3007	mSize_ = 2*lNumber_+1;
75	chuckv	3005
76	gezelter	3009	// Q can take values from 0 to 1
77	chuckv	3005
78	gezelter	3009	MinQ_ = 0.0;
79			MaxQ_ = 1.0;
80			deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81	gezelter	3007	Q_histogram_.resize(nbins);
82	gezelter	3009
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	gezelter	3007	W_histogram_.resize(nbins);
90	chuckv	3005
91	gezelter	3007	}
92	chuckv	3005
93	gezelter	3009	BondOrderParameter::~BondOrderParameter() {
94			Q_histogram_.clear();
95			W_histogram_.clear();
96			}
97
98	gezelter	3007	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	chuckv	3005
103	gezelter	3007	void BondOrderParameter::process() {
104			Molecule* mol;
105			Atom* atom;
106			RigidBody* rb;
107			SimInfo::MoleculeIterator mi;
108			Molecule::RigidBodyIterator rbIter;
109			Molecule::AtomIterator ai;
110			StuntDouble* sd;
111	gezelter	3010	RealType costheta;
112	gezelter	3007	RealType phi;
113			RealType r;
114			RealType dist;
115	gezelter	3010	std::map<int, ComplexType> QBar_lm;
116	gezelter	3007	RealType QSq_l;
117			RealType Q_l;
118			int nBonds;
119	gezelter	3010	SphericalHarmonic sphericalHarmonic;
120	gezelter	3007	int i, j;
121
122	gezelter	3008	// Set the l for the spherical harmonic, it doesn't change
123			sphericalHarmonic.setL(lNumber_);
124
125
126	gezelter	3007	DumpReader reader(info_, dumpFilename_);
127			int nFrames = reader.getNFrames();
128	gezelter	3009	frameCounter_ = 0;
129	chuckv	3005
130	gezelter	3007	for (int istep = 0; istep < nFrames; istep += step_) {
131			reader.readFrame(istep);
132	gezelter	3009	frameCounter_++;
133	gezelter	3007	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
134
135			if (evaluator_.isDynamic()) {
136			seleMan_.setSelectionSet(evaluator_.evaluate());
137			}
138	chuckv	3005
139	gezelter	3007	// update the positions of atoms which belong to the rigidbodies
140	chuckv	3005
141	gezelter	3007	for (mol = info_->beginMolecule(mi); mol != NULL;
142			mol = info_->nextMolecule(mi)) {
143			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
144			rb = mol->nextRigidBody(rbIter)) {
145			rb->updateAtoms();
146			}
147			}
148
149			// outer loop is over the selected StuntDoubles:
150	chuckv	3005
151	gezelter	3007	for (sd = seleMan_.beginSelected(i); sd != NULL;
152			sd = seleMan_.nextSelected(i)) {
153	chuckv	3005
154	gezelter	3007	// For this central atom, zero out nBonds and QBar_lm
155	chuckv	3005
156	gezelter	3007	nBonds = 0;
157
158			for (int m = -lNumber_; m <= lNumber_; m++) {
159			QBar_lm[m] = 0.0;
160			}
161
162			// inner loop is over all other atoms in the system:
163
164			for (mol = info_->beginMolecule(mi); mol != NULL;
165			mol = info_->nextMolecule(mi)) {
166			for (atom = mol->beginAtom(ai); atom != NULL;
167			atom = mol->nextAtom(ai)) {
168	chuckv	3005
169
170	gezelter	3007	Vector3d vec = sd->getPos() - atom->getPos();
171			currentSnapshot_->wrapVector(vec);
172
173			// Calculate "bonds" and build Q_lm(r) where
174			// Q_lm = Y_lm(theta(r),phi(r))
175			// The spherical harmonics are wrt any arbitrary coordinate
176			// system, we choose standard spherical coordinates
177
178			r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
179
180			// Check to see if neighbor is in bond cutoff
181
182			if (r < rCut_) {
183	gezelter	3010	costheta = vec.z() / r;
184			phi = atan2(vec.y(), vec.x());
185
186	gezelter	3007	for(int m = -lNumber_; m <= lNumber_; m++){
187			sphericalHarmonic.setM(m);
188	gezelter	3010	QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
189	gezelter	3007	}
190			nBonds++;
191			}
192			}
193			}
194
195	gezelter	3010	// Normalize Qbar2
196	gezelter	3007	for (int m = -lNumber_;m <= lNumber_; m++){
197			QBar_lm[m] /= nBonds;
198			}
199	chuckv	3005
200	gezelter	3007	// Find second order invariant Q_l
201	chuckv	3005
202	gezelter	3007	QSq_l = 0.0;
203			for (int m = -lNumber_; m <= lNumber_; m++){
204	gezelter	3010	QSq_l += norm(QBar_lm[m]);
205	gezelter	3007	}
206			Q_l = sqrt(QSq_l(4.0 NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
207
208			// Find Third Order Invariant W_l
209	chuckv	3005
210	gezelter	3007	// Make arrays for Wigner3jm
211			double* THRCOF = new double[mSize_];
212			// Variables for Wigner routine
213			double l_ = (double)lNumber_;
214	gezelter	3009	double m1Pass, m2Min, m2Max;
215	gezelter	3007	int error, m1, m2, m3;
216	gezelter	3008
217	gezelter	3010	ComplexType W_l;
218			ComplexType W_l_hat;
219	gezelter	3008	W_l = 0.0;
220	gezelter	3007	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
221			// Zero work array
222	gezelter	3008	for (int ii = 0; ii < mSize_; ii++){
223	gezelter	3007	THRCOF[i] = 0.0;
224			}
225			// Get Wigner coefficients
226	gezelter	3009	m1Pass = (double)m1;
227			Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
228	gezelter	3007	for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
229			m2 = floor(m2Min) + m_index - 1;
230			m3 = -m1-m2;
231	gezelter	3008	W_l += THRCOF[m_index]QBar_lm[m1+lNumber_]QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
232	gezelter	3007	}
233			}
234	chuckv	3005
235	gezelter	3008	W_l_hat = W_l / pow(QSq_l, 1.5);
236	chuckv	3005
237	gezelter	3007	// accumulate histogram data for Q_l and W_l_hat:
238	chuckv	3005
239	gezelter	3010	collectHistogram(Q_l, real(W_l_hat));
240	gezelter	3007
241	chuckv	3005	}
242	gezelter	3007	}
243
244			writeOrderParameter();
245
246			}
247	chuckv	3005
248
249	gezelter	3009	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
250	chuckv	3005
251	gezelter	3009	if (Q_l >= MinQ_ && Q_l < MaxQ_) {
252			int qbin = (Q_l - MinQ_) / deltaQ_;
253			Q_histogram_[qbin] += 1;
254			Qcount_++;
255			sumQ_ += Q_l;
256			sumQ2_ += Q_l * Q_l;
257			} else {
258			sprintf( painCave.errMsg,
259			"Q_l value outside reasonable range\n");
260			painCave.severity = OOPSE_ERROR;
261			painCave.isFatal = 1;
262			simError();
263	gezelter	3007	}
264	chuckv	3005
265	gezelter	3009	if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
266			int wbin = (W_l_hat - MinW_) / deltaW_;
267			W_histogram_[wbin] += 1;
268			Wcount_++;
269			sumW_ += W_l_hat;
270			sumW2_ += W_l_hat*W_l_hat;
271			} else {
272			sprintf( painCave.errMsg,
273			"W_l_hat value outside reasonable range\n");
274			painCave.severity = OOPSE_ERROR;
275			painCave.isFatal = 1;
276			simError();
277	chuckv	3005	}
278	gezelter	3009	}
279	chuckv	3005
280	gezelter	3007	void BondOrderParameter::writeOrderParameter() {
281	chuckv	3005
282	gezelter	3009	std::ofstream osq((getOutputFileName() + "q").c_str());
283	chuckv	3005
284	gezelter	3009	if (osq.is_open()) {
285	chuckv	3005
286	gezelter	3009	RealType qAvg = sumQ_ / (RealType) Qcount_;
287			RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
288
289			osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
290			osq << "# selection: (" << selectionScript_ << ")\n";
291			osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
292			osq << "# std. dev.: " << qStdDev << "\n";
293
294			// Normalize by number of frames and write it out:
295			for (int i = 0; i < Q_histogram_.size(); ++i) {
296			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
297			osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
298			}
299
300			osq.close();
301			} else {
302			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
303			(getOutputFileName() + "q").c_str());
304			painCave.isFatal = 1;
305			simError();
306	gezelter	3007	}
307	chuckv	3005
308	gezelter	3009	std::ofstream osw((getOutputFileName() + "w").c_str());
309	chuckv	3005
310	gezelter	3009	if (osw.is_open()) {
311	chuckv	3005
312	gezelter	3009	RealType wAvg = sumW_ / (RealType) Wcount_;
313			RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
314
315			osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
316			osw << "# selection: (" << selectionScript_ << ")\n";
317			osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
318			osw << "# std. dev.: " << wStdDev << "\n";
319
320			// Normalize by number of frames and write it out:
321			for (int i = 0; i < W_histogram_.size(); ++i) {
322			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
323			osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
324			}
325
326			osw.close();
327			} else {
328			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
329			(getOutputFileName() + "w").c_str());
330			painCave.isFatal = 1;
331			simError();
332			}
333			}
334	gezelter	3007	}