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_ = 3.0;
    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; 
        }

        // 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_ + 1.0));

        // 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[ii] = 0.0;
          }
          // Get Wigner coefficients
          m1Pass = (double)m1;

          Wigner3jm(&l_, &l_, &l_, 
                    &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_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" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\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" << (RealType)W_histogram_[i] / (RealType)Wcount_ << "\n";
      }
      
      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
  }
}
Revision:	1046
Committed:	Thu Sep 21 20:43:17 2006 UTC (18 years, 7 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/BondOrderParameter.cpp*
File size:	11290 byte(s)
Log Message:	more changes to BOP and SH
#	User	Rev	Content
1	chuckv	1038	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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	1039
49	chuckv	1038	#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	1042	#include "math/SphericalHarmonic.hpp"
55	gezelter	1041
56	chuckv	1038	namespace oopse {
57
58	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	1041	double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	1039
63	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	1038
65	gezelter	1039	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	1038	}
69
70	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	1038	lNumber_ = lNumber;
73			rCut_ = rCut;
74	gezelter	1039	mSize_ = 2*lNumber_+1;
75	chuckv	1038
76	gezelter	1041	// Q can take values from 0 to 1
77	chuckv	1038
78	gezelter	1041	MinQ_ = 0.0;
79	gezelter	1046	MaxQ_ = 3.0;
80	gezelter	1041	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81	gezelter	1039	Q_histogram_.resize(nbins);
82	gezelter	1041
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	1039	W_histogram_.resize(nbins);
90	chuckv	1038
91	gezelter	1039	}
92	chuckv	1038
93	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
94			Q_histogram_.clear();
95			W_histogram_.clear();
96			}
97
98	gezelter	1039	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	1038
103	gezelter	1039	void BondOrderParameter::process() {
104			Molecule* mol;
105			Atom* atom;
106			RigidBody* rb;
107	gezelter	1043	int myIndex;
108	gezelter	1039	SimInfo::MoleculeIterator mi;
109			Molecule::RigidBodyIterator rbIter;
110			Molecule::AtomIterator ai;
111			StuntDouble* sd;
112	gezelter	1043	Vector3d vec;
113	gezelter	1042	RealType costheta;
114	gezelter	1039	RealType phi;
115			RealType r;
116			RealType dist;
117	gezelter	1046	std::map<int,ComplexType> QBar_lm;
118	gezelter	1039	RealType QSq_l;
119			RealType Q_l;
120	gezelter	1043	ComplexType W_l;
121			ComplexType W_l_hat;
122	gezelter	1039	int nBonds;
123	gezelter	1042	SphericalHarmonic sphericalHarmonic;
124	gezelter	1039	int i, j;
125	gezelter	1043	// 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	gezelter	1040	// Set the l for the spherical harmonic, it doesn't change
133			sphericalHarmonic.setL(lNumber_);
134
135	gezelter	1039	DumpReader reader(info_, dumpFilename_);
136			int nFrames = reader.getNFrames();
137	gezelter	1041	frameCounter_ = 0;
138	chuckv	1038
139	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
140			reader.readFrame(istep);
141	gezelter	1041	frameCounter_++;
142	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
143
144			if (evaluator_.isDynamic()) {
145			seleMan_.setSelectionSet(evaluator_.evaluate());
146			}
147	chuckv	1038
148	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
149	chuckv	1038
150	gezelter	1039	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	chuckv	1038
160	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
161			sd = seleMan_.nextSelected(i)) {
162	chuckv	1038
163	gezelter	1043	myIndex = sd->getGlobalIndex();
164
165	gezelter	1039	// For this central atom, zero out nBonds and QBar_lm
166	chuckv	1038
167	gezelter	1039	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	chuckv	1038
180	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
181	chuckv	1038
182	gezelter	1043	vec = sd->getPos() - atom->getPos();
183			currentSnapshot_->wrapVector(vec);
184	gezelter	1042
185	gezelter	1043	// 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	gezelter	1039	}
206			}
207
208	gezelter	1042	// Normalize Qbar2
209	gezelter	1039	for (int m = -lNumber_;m <= lNumber_; m++){
210			QBar_lm[m] /= nBonds;
211			}
212	chuckv	1038
213	gezelter	1039	// Find second order invariant Q_l
214	chuckv	1038
215	gezelter	1039	QSq_l = 0.0;
216			for (int m = -lNumber_; m <= lNumber_; m++){
217	gezelter	1042	QSq_l += norm(QBar_lm[m]);
218	gezelter	1039	}
219	gezelter	1046
220	gezelter	1044	Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI /
221			(2.0*(RealType)lNumber_ + 1.0));
222	gezelter	1043
223	gezelter	1039	// Find Third Order Invariant W_l
224	gezelter	1043
225	gezelter	1040	W_l = 0.0;
226	gezelter	1039	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
227			// Zero work array
228	gezelter	1040	for (int ii = 0; ii < mSize_; ii++){
229	gezelter	1046	THRCOF[ii] = 0.0;
230	gezelter	1039	}
231			// Get Wigner coefficients
232	gezelter	1041	m1Pass = (double)m1;
233	gezelter	1046
234			Wigner3jm(&l_, &l_, &l_,
235			&m1Pass, &m2Min, &m2Max,
236			THRCOF, &mSize_, &error);
237
238			for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
239			m2 = (int)floor(m2Min) + mmm;
240	gezelter	1039	m3 = -m1-m2;
241	gezelter	1046	W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
242	gezelter	1039	}
243			}
244	gezelter	1043
245	gezelter	1040	W_l_hat = W_l / pow(QSq_l, 1.5);
246	gezelter	1043
247	gezelter	1039	// accumulate histogram data for Q_l and W_l_hat:
248	chuckv	1038
249	gezelter	1043	std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
250	gezelter	1042	collectHistogram(Q_l, real(W_l_hat));
251	gezelter	1039
252	chuckv	1038	}
253	gezelter	1039	}
254
255			writeOrderParameter();
256
257			}
258	chuckv	1038
259
260	gezelter	1041	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
261	chuckv	1038
262	gezelter	1041	if (Q_l >= MinQ_ && Q_l < MaxQ_) {
263			int qbin = (Q_l - MinQ_) / deltaQ_;
264			Q_histogram_[qbin] += 1;
265			Qcount_++;
266			sumQ_ += Q_l;
267			sumQ2_ += Q_l * Q_l;
268			} else {
269			sprintf( painCave.errMsg,
270			"Q_l value outside reasonable range\n");
271			painCave.severity = OOPSE_ERROR;
272			painCave.isFatal = 1;
273			simError();
274	gezelter	1039	}
275	chuckv	1038
276	gezelter	1041	if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
277			int wbin = (W_l_hat - MinW_) / deltaW_;
278			W_histogram_[wbin] += 1;
279			Wcount_++;
280			sumW_ += W_l_hat;
281			sumW2_ += W_l_hat*W_l_hat;
282			} else {
283			sprintf( painCave.errMsg,
284			"W_l_hat value outside reasonable range\n");
285			painCave.severity = OOPSE_ERROR;
286			painCave.isFatal = 1;
287			simError();
288	chuckv	1038	}
289	gezelter	1041	}
290	chuckv	1038
291	gezelter	1039	void BondOrderParameter::writeOrderParameter() {
292	chuckv	1038
293	gezelter	1041	std::ofstream osq((getOutputFileName() + "q").c_str());
294	chuckv	1038
295	gezelter	1041	if (osq.is_open()) {
296	chuckv	1038
297	gezelter	1041	RealType qAvg = sumQ_ / (RealType) Qcount_;
298			RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
299
300			osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
301			osq << "# selection: (" << selectionScript_ << ")\n";
302			osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
303			osq << "# std. dev.: " << qStdDev << "\n";
304
305			// Normalize by number of frames and write it out:
306			for (int i = 0; i < Q_histogram_.size(); ++i) {
307			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
308	gezelter	1046	osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
309	gezelter	1041	}
310
311			osq.close();
312			} else {
313			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
314			(getOutputFileName() + "q").c_str());
315			painCave.isFatal = 1;
316			simError();
317	gezelter	1039	}
318	chuckv	1038
319	gezelter	1041	std::ofstream osw((getOutputFileName() + "w").c_str());
320	chuckv	1038
321	gezelter	1041	if (osw.is_open()) {
322	chuckv	1038
323	gezelter	1041	RealType wAvg = sumW_ / (RealType) Wcount_;
324			RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
325
326			osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
327			osw << "# selection: (" << selectionScript_ << ")\n";
328			osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
329			osw << "# std. dev.: " << wStdDev << "\n";
330
331			// Normalize by number of frames and write it out:
332			for (int i = 0; i < W_histogram_.size(); ++i) {
333			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
334	gezelter	1046	osw << Wval << "\t" << (RealType)W_histogram_[i] / (RealType)Wcount_ << "\n";
335	gezelter	1041	}
336
337			osw.close();
338			} else {
339			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
340			(getOutputFileName() + "w").c_str());
341			painCave.isFatal = 1;
342			simError();
343			}
344			}
345	gezelter	1039	}