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 lMax, 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:

    lMax_ = lMax;
    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_ = -0.18;
    MaxW_ = 0.18;
    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::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);
    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;
        }
        collectHistogram(q_l);
        
        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) {

    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();  
      }
    }

  }  


  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
    
    std::ofstream os(getOutputFileName().c_str());
    
    if (os.is_open()) {
      
      os << "# Bond Order Parameters\n";
      os << "# selection: (" << selectionScript_ << ")\n";
      for (int l = 0; l <= lMax_; l++) {
        os << "# \n";
        os << "# <Q_" << l << ">: " << Q[l] << "\n";
        os << "# <W_" << l << ">: " << real(What[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_;               
        os << Qval;
        for (int l = 0; l <= lMax_; l++) {
          os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
        }
        os << "\n";
      }

      os.close();

    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();  
    }
  }
}
Revision:	1051
Committed:	Mon Sep 25 22:08:33 2006 UTC (18 years, 7 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/BondOrderParameter.cpp*
File size:	10926 byte(s)
Log Message:	fixing bond order parameter code
#	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	1041
55	chuckv	1038	namespace oopse {
56
57	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
58			const std::string& filename,
59			const std::string& sele,
60	gezelter	1051	double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61	gezelter	1039
62	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
63	chuckv	1038
64	gezelter	1039	evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67	chuckv	1038	}
68
69	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
70
71	gezelter	1051	lMax_ = lMax;
72	chuckv	1038	rCut_ = rCut;
73	gezelter	1051	nBins_ = nbins;
74			Qcount_.resize(lMax_+1);
75			Wcount_.resize(lMax_+1);
76	gezelter	1048
77			// Q can take values from 0 to 1
78
79			MinQ_ = 0.0;
80	gezelter	1051	MaxQ_ = 1.1;
81	gezelter	1048	deltaQ_ = (MaxQ_ - MinQ_) / 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	gezelter	1039	}
90	chuckv	1038
91	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
92	gezelter	1048	Q_histogram_.clear();
93			W_histogram_.clear();
94	gezelter	1041	}
95
96	gezelter	1048	void BondOrderParameter::initalizeHistogram() {
97	gezelter	1051	for (int bin = 0; bin < nBins_; bin++) {
98			for (int l = 0; l <= lMax_; l++) {
99			Q_histogram_[std::make_pair(bin,l)] = 0;
100			W_histogram_[std::make_pair(bin,l)] = 0;
101			}
102			}
103	gezelter	1048	}
104
105	gezelter	1039	void BondOrderParameter::process() {
106			Molecule* mol;
107			Atom* atom;
108			RigidBody* rb;
109	gezelter	1043	int myIndex;
110	gezelter	1039	SimInfo::MoleculeIterator mi;
111			Molecule::RigidBodyIterator rbIter;
112			Molecule::AtomIterator ai;
113			StuntDouble* sd;
114	gezelter	1043	Vector3d vec;
115	gezelter	1042	RealType costheta;
116	gezelter	1039	RealType phi;
117			RealType r;
118			RealType dist;
119	gezelter	1051	std::map<std::pair<int,int>,ComplexType> q;
120			std::vector<RealType> q_l;
121			std::map<std::pair<int,int>,ComplexType> QBar;
122			std::vector<RealType> Q2;
123			std::vector<RealType> Q;
124			std::vector<ComplexType> W;
125			std::vector<ComplexType> W_hat;
126	gezelter	1048	int nBonds, Nbonds;
127	gezelter	1042	SphericalHarmonic sphericalHarmonic;
128	gezelter	1039	int i, j;
129	gezelter	1043	// Make arrays for Wigner3jm
130	gezelter	1051	double* THRCOF = new double[2*lMax_+1];
131	gezelter	1043	// Variables for Wigner routine
132	gezelter	1051	double lPass, m1Pass, m2Min, m2Max;
133			int error, m1, m2, m3, mSize;
134			mSize = 2*lMax_+1;
135	gezelter	1043
136	gezelter	1039	DumpReader reader(info_, dumpFilename_);
137			int nFrames = reader.getNFrames();
138	gezelter	1041	frameCounter_ = 0;
139	chuckv	1038
140	gezelter	1051	q_l.resize(lMax_+1);
141			Q2.resize(lMax_+1);
142			Q.resize(lMax_+1);
143			W.resize(lMax_+1);
144			W_hat.resize(lMax_+1);
145
146	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
147			reader.readFrame(istep);
148	gezelter	1041	frameCounter_++;
149	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
150
151			if (evaluator_.isDynamic()) {
152			seleMan_.setSelectionSet(evaluator_.evaluate());
153			}
154	chuckv	1038
155	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
156	chuckv	1038
157	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
158			mol = info_->nextMolecule(mi)) {
159			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
160			rb = mol->nextRigidBody(rbIter)) {
161			rb->updateAtoms();
162			}
163	gezelter	1048	}
164
165	gezelter	1039	// outer loop is over the selected StuntDoubles:
166	chuckv	1038
167	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
168			sd = seleMan_.nextSelected(i)) {
169	chuckv	1038
170	gezelter	1043	myIndex = sd->getGlobalIndex();
171	gezelter	1048	nBonds = 0;
172	gezelter	1051
173			for (int l = 0; l <= lMax_; l++) {
174			for (int m = -l; m <= l; m++) {
175			q[std::make_pair(l,m)] = 0.0;
176			}
177	gezelter	1048	}
178	gezelter	1039
179			// inner loop is over all other atoms in the system:
180
181			for (mol = info_->beginMolecule(mi); mol != NULL;
182			mol = info_->nextMolecule(mi)) {
183			for (atom = mol->beginAtom(ai); atom != NULL;
184			atom = mol->nextAtom(ai)) {
185	chuckv	1038
186	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
187	chuckv	1038
188	gezelter	1043	vec = sd->getPos() - atom->getPos();
189			currentSnapshot_->wrapVector(vec);
190	gezelter	1042
191	gezelter	1043	// Calculate "bonds" and build Q_lm(r) where
192			// Q_lm = Y_lm(theta(r),phi(r))
193			// The spherical harmonics are wrt any arbitrary coordinate
194			// system, we choose standard spherical coordinates
195
196			r = vec.length();
197
198			// Check to see if neighbor is in bond cutoff
199
200			if (r < rCut_) {
201			costheta = vec.z() / r;
202			phi = atan2(vec.y(), vec.x());
203	gezelter	1051
204			for (int l = 0; l <= lMax_; l++) {
205			sphericalHarmonic.setL(l);
206			for(int m = -l; m <= l; m++){
207			sphericalHarmonic.setM(m);
208			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
209			}
210	gezelter	1043	}
211			nBonds++;
212			}
213			}
214	gezelter	1039	}
215			}
216	gezelter	1051
217
218			for (int l = 0; l <= lMax_; l++) {
219			q_l[l] = 0.0;
220			for(int m = -l; m <= l; m++) {
221			q_l[l] += norm(q[std::make_pair(l,m)]);
222			}
223			q_l[l] = 4.0NumericConstant::PI/(RealType)(2*l + 1);
224			q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
225			}
226			collectHistogram(q_l);
227
228	gezelter	1048	Nbonds += nBonds;
229	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
230			for (int m = -l; m <= l; m++) {
231			QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
232			}
233	gezelter	1048	}
234			}
235	gezelter	1047	}
236	gezelter	1051
237	gezelter	1047	// Normalize Qbar2
238	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
239			for (int m = -l; m <= l; m++){
240			QBar[std::make_pair(l,m)] /= Nbonds;
241			}
242	gezelter	1039	}
243
244	gezelter	1047	// Find second order invariant Q_l
245	gezelter	1039
246	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
247			Q2[l] = 0.0;
248			for (int m = -l; m <= l; m++){
249			Q2[l] += norm(QBar[std::make_pair(l,m)]);
250			}
251			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
252	gezelter	1039	}
253	gezelter	1047
254	gezelter	1051
255	gezelter	1047
256			// Find Third Order Invariant W_l
257
258	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
259			W[l] = 0.0;
260			lPass = (double)l;
261			for (int m1 = -l; m1 <= l; m1++) {
262			// Zero work array
263			for (int ii = 0; ii < 2*l + 1; ii++){
264			THRCOF[ii] = 0.0;
265			}
266			// Get Wigner coefficients
267			m1Pass = (double)m1;
268
269			Wigner3jm(&lPass, &lPass, &lPass,
270			&m1Pass, &m2Min, &m2Max,
271			THRCOF, &mSize, &error);
272
273			for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
274			m2 = (int)floor(m2Min) + mmm;
275			m3 = -m1-m2;
276			W[l] += THRCOF[mmm] *
277			QBar[std::make_pair(l,m1)] *
278			QBar[std::make_pair(l,m2)] *
279			QBar[std::make_pair(l,m3)];
280			}
281	gezelter	1047	}
282	gezelter	1041
283	gezelter	1051	W_hat[l] = W[l] / pow(Q2[l], 1.5);
284	gezelter	1039	}
285	gezelter	1047
286	gezelter	1051	writeOrderParameter(Q, W_hat);
287	gezelter	1047	}
288	chuckv	1038
289	gezelter	1051	void BondOrderParameter::collectHistogram(std::vector<RealType> q) {
290	chuckv	1038
291	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
292			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
293			int qbin = (q[l] - MinQ_) / deltaQ_;
294			Q_histogram_[std::make_pair(qbin,l)] += 1;
295			Qcount_[l]++;
296			} else {
297			sprintf( painCave.errMsg,
298			"q_l value outside reasonable range\n");
299			painCave.severity = OOPSE_ERROR;
300			painCave.isFatal = 1;
301			simError();
302			}
303	gezelter	1048	}
304
305			}
306
307
308	gezelter	1051	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) {
309
310	gezelter	1047	std::ofstream os(getOutputFileName().c_str());
311	gezelter	1051
312	gezelter	1047	if (os.is_open()) {
313	gezelter	1041
314	gezelter	1047	os << "# Bond Order Parameters\n";
315			os << "# selection: (" << selectionScript_ << ")\n";
316	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
317			os << "# \n";
318			os << "# <Q_" << l << ">: " << Q[l] << "\n";
319			os << "# <W_" << l << ">: " << real(What[l]) << "\n";
320			}
321	gezelter	1048	// Normalize by number of frames and write it out:
322	gezelter	1051	for (int i = 0; i < nBins_; ++i) {
323			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
324			os << Qval;
325			for (int l = 0; l <= lMax_; l++) {
326			os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
327			}
328			os << "\n";
329	gezelter	1048	}
330
331	gezelter	1047	os.close();
332
333	gezelter	1041	} else {
334			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
335	gezelter	1047	getOutputFileName().c_str());
336	gezelter	1041	painCave.isFatal = 1;
337			simError();
338			}
339			}
340	gezelter	1039	}