applications/staticProps/BOPofR.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.
 *
 *  BondOrderParameter.cpp
 *  OOPSE-4
 *
 *  Created by J. Daniel Gezelter on 09/26/06.
 *  @author  J. Daniel Gezelter
 *  @version $Id: BOPofR.cpp,v 1.2 2007-05-29 22:50:14 chuckv Exp $
 *
 */
 
#include "applications/staticProps/BOPofR.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"


namespace oopse {

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

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

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

    rCut_ = rCut;
    nBins_ = nbins;
    len_ = len;
        
    deltaR_ = len_/nBins_;
    RCount_.resize(nBins_);
    WofR_.resize(nBins_);
    QofR_.resize(nBins_);

        for (int i = 0; i < nBins_; i++){
                RCount_[i] = 0;
                WofR_[i] = 0;
                QofR_[i] = 0;
        }
        
    // Make arrays for Wigner3jm
    double* THRCOF = new double[2*lMax_+1];
    // Variables for Wigner routine
    double lPass, m1Pass, m2m, m2M;
    int error, mSize;
    mSize = 2*lMax_+1;

    for (int l = 0; l <= lMax_; l++) {
      lPass = (double)l;
      for (int m1 = -l; m1 <= l; m1++) {
        m1Pass = (double)m1;

        std::pair<int,int> lm = std::make_pair(l, m1);
        
        // Zero work array
        for (int ii = 0; ii < 2*l + 1; ii++){
          THRCOF[ii] = 0.0;
        }

        // Get Wigner coefficients
        Wigner3jm(&lPass, &lPass, &lPass, 
                  &m1Pass, &m2m, &m2M, 
                  THRCOF, &mSize, &error);
        
        m2Min[lm] = (int)floor(m2m);
        m2Max[lm] = (int)floor(m2M);
        
        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
          w3j[lm].push_back(THRCOF[mmm]);
        }
      }
    }

    delete [] THRCOF;
    THRCOF = NULL;      
        
  }
  
  BOPofR::~BOPofR() {
          /*
        std::cerr << "Freeing stuff" << std::endl;
    for (int l = 0; l <= lMax_; l++) {
      for (int m = -l; m <= l; m++) {
        w3j[std::make_pair(l,m)].clear();
      }
    }
        std::cerr << "w3j made free...." << std::endl;
   for (int bin = 0; bin < nBins_; bin++) {
                QofR_[bin].clear();
                WofR_[bin].clear();
                RCount_[bin].clear();
    }
        std::cout << "R arrays made free...." << std::endl;
   w3j.clear();
    m2Min.clear();
    m2Max.clear();
    RCount_.clear();
    WofR_.clear();
    QofR_.clear();
 */
  }

  
  void BOPofR::initalizeHistogram() {
        for (int i = 0; i < nBins_; i++){
                RCount_[i] = 0;
                WofR_[i] = 0;
                QofR_[i] = 0;
        }
  }


  void BOPofR::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;
    Vector3d rCOM;
    RealType distCOM;
    Vector3d pos;
    Vector3d CenterOfMass;
    std::map<std::pair<int,int>,ComplexType> q;
    std::vector<RealType> q_l;
    std::vector<RealType> q2;
    std::vector<ComplexType> w;
    std::vector<ComplexType> w_hat;
    std::map<std::pair<int,int>,ComplexType> QBar;
    std::vector<RealType> Q2;
    std::vector<RealType> Q;
    std::vector<ComplexType> W;
    std::vector<ComplexType> W_hat;
    int nBonds, Nbonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;

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

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

    Q2.resize(lMax_+1);
    Q.resize(lMax_+1);
    W.resize(lMax_+1);
    W_hat.resize(lMax_+1);
    Nbonds = 0;

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      CenterOfMass = info_->getCom();
      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;
          }
        }
        pos = sd->getPos();
        rCOM = CenterOfMass - pos;
        if (usePeriodicBoundaryConditions_) 
          currentSnapshot_->wrapVector(rCOM);
        distCOM = rCOM.length();

        // 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 = pos - atom->getPos();       

              if (usePeriodicBoundaryConditions_) 
                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++) {
          q2[l] = 0.0;
          for (int m = -l; m <= l; m++){
            q[std::make_pair(l,m)] /= (RealType)nBonds;            
            q2[l] += norm(q[std::make_pair(l,m)]);
          }
          q_l[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;
          for (int m1 = -l; m1 <= l; m1++) {
            std::pair<int,int> lm = std::make_pair(l, m1);
            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
              int m2 = m2Min[lm] + mmm;
              int m3 = -m1-m2;
              w[l] += w3j[lm][mmm] * q[lm] * 
                q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
            }
          }
          
          w_hat[l] = w[l] / pow(q2[l], 1.5);
        }

        collectHistogram(q_l, w_hat, distCOM);
                
                printf( "%s  %18.10g %18.10g %18.10g %18.10g \n", sd->getType().c_str(),pos[0],pos[1],pos[2],real(w_hat[6]));

      }
    }
        
    writeOrderParameter();    
  }

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

    if ( distCOM < len_){
      // Figure out where this distance goes...
      int whichBin = distCOM / deltaR_;
      RCount_[whichBin]++;

      if(real(what[6]) < -0.15){                                
                WofR_[whichBin]++;
      }
          if(q[6] > 0.5){
        QofR_[whichBin]++;
          }
    }  

  }

  void BOPofR::writeOrderParameter() {
    
    std::ofstream osq((getOutputFileName() + "qr").c_str());

    if (osq.is_open()) {
      
      // Normalize by number of frames and write it out:
          
      for (int i = 0; i < nBins_; ++i) {
        RealType Rval = (i + 0.5) * deltaR_;               
        osq << Rval;
                if (RCount_[i] == 0){
                        osq << "\t" << 0;
                        osq << "\n";
                }else{
                osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i];        
                osq << "\n";
                }
      }

      osq.close();

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

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

    if (osw.is_open()) {
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Rval = deltaR_ * (i + 0.5);               
        osw << Rval;
                if (RCount_[i] == 0){
                        osw << "\t" << 0;
                        osw << "\n";
                }else{
                osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i];
                osw << "\n";
                }
      }

      osw.close();
    } else {
      sprintf(painCave.errMsg, "BOPofR: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    
    }
        
  }
}
Revision:	3137
Committed:	Tue May 29 22:50:14 2007 UTC (17 years, 3 months ago) by chuckv
File size:	11512 byte(s)
Log Message:	Removed CGAL from OOPSE and replaced it with qhull.
#	User	Rev	Content
1	chuckv	3128	/*
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			* BondOrderParameter.cpp
42			* OOPSE-4
43			*
44			* Created by J. Daniel Gezelter on 09/26/06.
45			* @author J. Daniel Gezelter
46	chuckv	3137	* @version $Id: BOPofR.cpp,v 1.2 2007-05-29 22:50:14 chuckv Exp $
47	chuckv	3128	*
48			*/
49
50			#include "applications/staticProps/BOPofR.hpp"
51			#include "utils/simError.h"
52			#include "io/DumpReader.hpp"
53			#include "primitives/Molecule.hpp"
54			#include "utils/NumericConstant.hpp"
55
56
57			namespace oopse {
58
59			BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut,
60			int nbins, RealType len) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61
62			setOutputName(getPrefix(filename) + ".bo");
63
64			evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67			}
68
69			// Set up cutoff radius and order of the Legendre Polynomial:
70
71			rCut_ = rCut;
72			nBins_ = nbins;
73			len_ = len;
74
75			deltaR_ = len_/nBins_;
76			RCount_.resize(nBins_);
77			WofR_.resize(nBins_);
78			QofR_.resize(nBins_);
79	chuckv	3137
80			for (int i = 0; i < nBins_; i++){
81			RCount_[i] = 0;
82			WofR_[i] = 0;
83			QofR_[i] = 0;
84			}
85	chuckv	3128
86			// Make arrays for Wigner3jm
87			double* THRCOF = new double[2*lMax_+1];
88			// Variables for Wigner routine
89			double lPass, m1Pass, m2m, m2M;
90			int error, mSize;
91			mSize = 2*lMax_+1;
92
93			for (int l = 0; l <= lMax_; l++) {
94			lPass = (double)l;
95			for (int m1 = -l; m1 <= l; m1++) {
96			m1Pass = (double)m1;
97
98			std::pair<int,int> lm = std::make_pair(l, m1);
99
100			// Zero work array
101			for (int ii = 0; ii < 2*l + 1; ii++){
102			THRCOF[ii] = 0.0;
103			}
104
105			// Get Wigner coefficients
106			Wigner3jm(&lPass, &lPass, &lPass,
107			&m1Pass, &m2m, &m2M,
108			THRCOF, &mSize, &error);
109
110			m2Min[lm] = (int)floor(m2m);
111			m2Max[lm] = (int)floor(m2M);
112
113			for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
114			w3j[lm].push_back(THRCOF[mmm]);
115			}
116			}
117			}
118
119			delete [] THRCOF;
120	chuckv	3137	THRCOF = NULL;
121	chuckv	3128
122			}
123
124			BOPofR::~BOPofR() {
125			/*
126			std::cerr << "Freeing stuff" << std::endl;
127			for (int l = 0; l <= lMax_; l++) {
128			for (int m = -l; m <= l; m++) {
129			w3j[std::make_pair(l,m)].clear();
130			}
131			}
132			std::cerr << "w3j made free...." << std::endl;
133			for (int bin = 0; bin < nBins_; bin++) {
134			QofR_[bin].clear();
135			WofR_[bin].clear();
136			RCount_[bin].clear();
137			}
138			std::cout << "R arrays made free...." << std::endl;
139			w3j.clear();
140			m2Min.clear();
141			m2Max.clear();
142			RCount_.clear();
143			WofR_.clear();
144			QofR_.clear();
145			*/
146			}
147
148
149			void BOPofR::initalizeHistogram() {
150	chuckv	3137	for (int i = 0; i < nBins_; i++){
151			RCount_[i] = 0;
152			WofR_[i] = 0;
153			QofR_[i] = 0;
154			}
155	chuckv	3128	}
156
157
158			void BOPofR::process() {
159			Molecule* mol;
160			Atom* atom;
161			RigidBody* rb;
162			int myIndex;
163			SimInfo::MoleculeIterator mi;
164			Molecule::RigidBodyIterator rbIter;
165			Molecule::AtomIterator ai;
166			StuntDouble* sd;
167			Vector3d vec;
168			RealType costheta;
169			RealType phi;
170			RealType r;
171			RealType dist;
172			Vector3d rCOM;
173			RealType distCOM;
174			Vector3d pos;
175			Vector3d CenterOfMass;
176			std::map<std::pair<int,int>,ComplexType> q;
177			std::vector<RealType> q_l;
178			std::vector<RealType> q2;
179			std::vector<ComplexType> w;
180			std::vector<ComplexType> w_hat;
181			std::map<std::pair<int,int>,ComplexType> QBar;
182			std::vector<RealType> Q2;
183			std::vector<RealType> Q;
184			std::vector<ComplexType> W;
185			std::vector<ComplexType> W_hat;
186			int nBonds, Nbonds;
187			SphericalHarmonic sphericalHarmonic;
188			int i, j;
189
190			DumpReader reader(info_, dumpFilename_);
191			int nFrames = reader.getNFrames();
192			frameCounter_ = 0;
193
194			q_l.resize(lMax_+1);
195			q2.resize(lMax_+1);
196			w.resize(lMax_+1);
197			w_hat.resize(lMax_+1);
198
199			Q2.resize(lMax_+1);
200			Q.resize(lMax_+1);
201			W.resize(lMax_+1);
202			W_hat.resize(lMax_+1);
203			Nbonds = 0;
204
205			for (int istep = 0; istep < nFrames; istep += step_) {
206			reader.readFrame(istep);
207			frameCounter_++;
208			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
209			CenterOfMass = info_->getCom();
210			if (evaluator_.isDynamic()) {
211			seleMan_.setSelectionSet(evaluator_.evaluate());
212			}
213
214			// update the positions of atoms which belong to the rigidbodies
215
216			for (mol = info_->beginMolecule(mi); mol != NULL;
217			mol = info_->nextMolecule(mi)) {
218			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
219			rb = mol->nextRigidBody(rbIter)) {
220			rb->updateAtoms();
221			}
222			}
223
224			// outer loop is over the selected StuntDoubles:
225
226			for (sd = seleMan_.beginSelected(i); sd != NULL;
227			sd = seleMan_.nextSelected(i)) {
228
229			myIndex = sd->getGlobalIndex();
230
231			nBonds = 0;
232
233			for (int l = 0; l <= lMax_; l++) {
234			for (int m = -l; m <= l; m++) {
235			q[std::make_pair(l,m)] = 0.0;
236			}
237			}
238			pos = sd->getPos();
239			rCOM = CenterOfMass - pos;
240			if (usePeriodicBoundaryConditions_)
241			currentSnapshot_->wrapVector(rCOM);
242			distCOM = rCOM.length();
243
244			// inner loop is over all other atoms in the system:
245
246			for (mol = info_->beginMolecule(mi); mol != NULL;
247			mol = info_->nextMolecule(mi)) {
248			for (atom = mol->beginAtom(ai); atom != NULL;
249			atom = mol->nextAtom(ai)) {
250
251			if (atom->getGlobalIndex() != myIndex) {
252			vec = pos - atom->getPos();
253
254			if (usePeriodicBoundaryConditions_)
255			currentSnapshot_->wrapVector(vec);
256
257			// Calculate "bonds" and build Q_lm(r) where
258			// Q_lm = Y_lm(theta(r),phi(r))
259			// The spherical harmonics are wrt any arbitrary coordinate
260			// system, we choose standard spherical coordinates
261
262			r = vec.length();
263
264			// Check to see if neighbor is in bond cutoff
265
266			if (r < rCut_) {
267			costheta = vec.z() / r;
268			phi = atan2(vec.y(), vec.x());
269
270			for (int l = 0; l <= lMax_; l++) {
271			sphericalHarmonic.setL(l);
272			for(int m = -l; m <= l; m++){
273			sphericalHarmonic.setM(m);
274			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
275			}
276			}
277			nBonds++;
278			}
279			}
280			}
281			}
282
283
284			for (int l = 0; l <= lMax_; l++) {
285			q2[l] = 0.0;
286			for (int m = -l; m <= l; m++){
287			q[std::make_pair(l,m)] /= (RealType)nBonds;
288			q2[l] += norm(q[std::make_pair(l,m)]);
289			}
290			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
291			}
292
293			// Find Third Order Invariant W_l
294
295			for (int l = 0; l <= lMax_; l++) {
296			w[l] = 0.0;
297			for (int m1 = -l; m1 <= l; m1++) {
298			std::pair<int,int> lm = std::make_pair(l, m1);
299			for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
300			int m2 = m2Min[lm] + mmm;
301			int m3 = -m1-m2;
302			w[l] += w3j[lm][mmm] * q[lm] *
303			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
304			}
305			}
306
307			w_hat[l] = w[l] / pow(q2[l], 1.5);
308			}
309
310			collectHistogram(q_l, w_hat, distCOM);
311	chuckv	3137
312			printf( "%s %18.10g %18.10g %18.10g %18.10g \n", sd->getType().c_str(),pos[0],pos[1],pos[2],real(w_hat[6]));
313
314	chuckv	3128	}
315			}
316
317			writeOrderParameter();
318			}
319
320			void BOPofR::collectHistogram(std::vector<RealType> q,
321			std::vector<ComplexType> what, RealType distCOM) {
322
323			if ( distCOM < len_){
324			// Figure out where this distance goes...
325			int whichBin = distCOM / deltaR_;
326	chuckv	3137	RCount_[whichBin]++;
327
328			if(real(what[6]) < -0.15){
329			WofR_[whichBin]++;
330	chuckv	3128	}
331	chuckv	3137	if(q[6] > 0.5){
332			QofR_[whichBin]++;
333			}
334	chuckv	3128	}
335
336			}
337
338			void BOPofR::writeOrderParameter() {
339
340			std::ofstream osq((getOutputFileName() + "qr").c_str());
341
342			if (osq.is_open()) {
343
344			// Normalize by number of frames and write it out:
345
346			for (int i = 0; i < nBins_; ++i) {
347			RealType Rval = (i + 0.5) * deltaR_;
348			osq << Rval;
349	chuckv	3137	if (RCount_[i] == 0){
350			osq << "\t" << 0;
351			osq << "\n";
352			}else{
353			osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i];
354			osq << "\n";
355			}
356	chuckv	3128	}
357
358			osq.close();
359
360			} else {
361			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
362			(getOutputFileName() + "q").c_str());
363			painCave.isFatal = 1;
364			simError();
365			}
366
367			std::ofstream osw((getOutputFileName() + "wr").c_str());
368
369			if (osw.is_open()) {
370			// Normalize by number of frames and write it out:
371			for (int i = 0; i < nBins_; ++i) {
372			RealType Rval = deltaR_ * (i + 0.5);
373			osw << Rval;
374	chuckv	3137	if (RCount_[i] == 0){
375			osw << "\t" << 0;
376			osw << "\n";
377			}else{
378			osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i];
379			osw << "\n";
380			}
381	chuckv	3128	}
382
383			osw.close();
384			} else {
385			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
386			(getOutputFileName() + "w").c_str());
387			painCave.isFatal = 1;
388			simError();
389
390			}
391
392			}
393			}