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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by J. Daniel Gezelter on 09/26/06.
 *  @author  J. Daniel Gezelter
 *  @version $Id$
 *
 */
 
#include "applications/staticProps/BOPofR.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "math/Wigner3jm.hpp"
#include "brains/Thermo.hpp"

using namespace MATPACK;
namespace OpenMD {

  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
    RealType* THRCOF = new RealType[2*lMax_+1];
    // Variables for Wigner routine
    RealType lPass, m1Pass, m2m, m2M;
    int error, mSize;
    mSize = 2*lMax_+1;

    for (int l = 0; l <= lMax_; l++) {
      lPass = (RealType)l;
      for (int m1 = -l; m1 <= l; m1++) {
        m1Pass = (RealType)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::initializeHistogram() {
        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;
    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::vector<RealType> Q2;
    std::vector<RealType> Q;
    std::vector<ComplexType> W;
    std::vector<ComplexType> W_hat;
    int nBonds;
    SphericalHarmonic sphericalHarmonic;
    int i;
    
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    frameCounter_ = 0;

    Thermo thermo(info_);

    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);

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      CenterOfMass = thermo.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], RealType(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 = int(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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	11555 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	chuckv	1128	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1128	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1128	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32	gezelter	1390	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	chuckv	1128	* Created by J. Daniel Gezelter on 09/26/06.
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	chuckv	1128	*
45			*/
46
47			#include "applications/staticProps/BOPofR.hpp"
48			#include "utils/simError.h"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51			#include "utils/NumericConstant.hpp"
52	gezelter	1782	#include "math/Wigner3jm.hpp"
53			#include "brains/Thermo.hpp"
54	chuckv	1128
55	gezelter	1782	using namespace MATPACK;
56	gezelter	1390	namespace OpenMD {
57	chuckv	1128
58			BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut,
59			int nbins, RealType len) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
60
61			setOutputName(getPrefix(filename) + ".bo");
62
63			evaluator_.loadScriptString(sele);
64			if (!evaluator_.isDynamic()) {
65			seleMan_.setSelectionSet(evaluator_.evaluate());
66			}
67
68			// Set up cutoff radius and order of the Legendre Polynomial:
69
70			rCut_ = rCut;
71			nBins_ = nbins;
72			len_ = len;
73
74			deltaR_ = len_/nBins_;
75			RCount_.resize(nBins_);
76			WofR_.resize(nBins_);
77			QofR_.resize(nBins_);
78	chuckv	1137
79			for (int i = 0; i < nBins_; i++){
80			RCount_[i] = 0;
81			WofR_[i] = 0;
82			QofR_[i] = 0;
83			}
84	chuckv	1128
85			// Make arrays for Wigner3jm
86	gezelter	1782	RealType* THRCOF = new RealType[2*lMax_+1];
87	chuckv	1128	// Variables for Wigner routine
88	gezelter	1782	RealType lPass, m1Pass, m2m, m2M;
89	chuckv	1128	int error, mSize;
90			mSize = 2*lMax_+1;
91
92			for (int l = 0; l <= lMax_; l++) {
93	gezelter	1782	lPass = (RealType)l;
94	chuckv	1128	for (int m1 = -l; m1 <= l; m1++) {
95	gezelter	1782	m1Pass = (RealType)m1;
96	chuckv	1128
97			std::pair<int,int> lm = std::make_pair(l, m1);
98
99			// Zero work array
100			for (int ii = 0; ii < 2*l + 1; ii++){
101			THRCOF[ii] = 0.0;
102			}
103
104			// Get Wigner coefficients
105	gezelter	1782	Wigner3jm(lPass, lPass, lPass,
106			m1Pass, m2m, m2M,
107			THRCOF, mSize, error);
108	chuckv	1128
109			m2Min[lm] = (int)floor(m2m);
110			m2Max[lm] = (int)floor(m2M);
111
112			for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
113			w3j[lm].push_back(THRCOF[mmm]);
114			}
115			}
116			}
117
118			delete [] THRCOF;
119	chuckv	1137	THRCOF = NULL;
120	chuckv	1128
121			}
122
123			BOPofR::~BOPofR() {
124			/*
125			std::cerr << "Freeing stuff" << std::endl;
126			for (int l = 0; l <= lMax_; l++) {
127			for (int m = -l; m <= l; m++) {
128			w3j[std::make_pair(l,m)].clear();
129			}
130			}
131			std::cerr << "w3j made free...." << std::endl;
132			for (int bin = 0; bin < nBins_; bin++) {
133			QofR_[bin].clear();
134			WofR_[bin].clear();
135			RCount_[bin].clear();
136			}
137			std::cout << "R arrays made free...." << std::endl;
138			w3j.clear();
139			m2Min.clear();
140			m2Max.clear();
141			RCount_.clear();
142			WofR_.clear();
143			QofR_.clear();
144			*/
145			}
146
147
148	jmichalk	1785	void BOPofR::initializeHistogram() {
149	chuckv	1137	for (int i = 0; i < nBins_; i++){
150			RCount_[i] = 0;
151			WofR_[i] = 0;
152			QofR_[i] = 0;
153			}
154	chuckv	1128	}
155
156
157			void BOPofR::process() {
158			Molecule* mol;
159			Atom* atom;
160			RigidBody* rb;
161			int myIndex;
162			SimInfo::MoleculeIterator mi;
163			Molecule::RigidBodyIterator rbIter;
164			Molecule::AtomIterator ai;
165			StuntDouble* sd;
166			Vector3d vec;
167			RealType costheta;
168			RealType phi;
169			RealType r;
170			Vector3d rCOM;
171			RealType distCOM;
172			Vector3d pos;
173			Vector3d CenterOfMass;
174			std::map<std::pair<int,int>,ComplexType> q;
175			std::vector<RealType> q_l;
176			std::vector<RealType> q2;
177			std::vector<ComplexType> w;
178			std::vector<ComplexType> w_hat;
179			std::vector<RealType> Q2;
180			std::vector<RealType> Q;
181			std::vector<ComplexType> W;
182			std::vector<ComplexType> W_hat;
183	gezelter	1793	int nBonds;
184	chuckv	1128	SphericalHarmonic sphericalHarmonic;
185	gezelter	1782	int i;
186
187	chuckv	1128	DumpReader reader(info_, dumpFilename_);
188			int nFrames = reader.getNFrames();
189			frameCounter_ = 0;
190
191	gezelter	1782	Thermo thermo(info_);
192
193	chuckv	1128	q_l.resize(lMax_+1);
194			q2.resize(lMax_+1);
195			w.resize(lMax_+1);
196			w_hat.resize(lMax_+1);
197
198			Q2.resize(lMax_+1);
199			Q.resize(lMax_+1);
200			W.resize(lMax_+1);
201			W_hat.resize(lMax_+1);
202
203			for (int istep = 0; istep < nFrames; istep += step_) {
204			reader.readFrame(istep);
205			frameCounter_++;
206			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
207	gezelter	1782	CenterOfMass = thermo.getCom();
208	chuckv	1128	if (evaluator_.isDynamic()) {
209			seleMan_.setSelectionSet(evaluator_.evaluate());
210			}
211
212			// update the positions of atoms which belong to the rigidbodies
213
214			for (mol = info_->beginMolecule(mi); mol != NULL;
215			mol = info_->nextMolecule(mi)) {
216			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
217			rb = mol->nextRigidBody(rbIter)) {
218			rb->updateAtoms();
219			}
220			}
221
222			// outer loop is over the selected StuntDoubles:
223
224			for (sd = seleMan_.beginSelected(i); sd != NULL;
225			sd = seleMan_.nextSelected(i)) {
226
227			myIndex = sd->getGlobalIndex();
228
229			nBonds = 0;
230
231			for (int l = 0; l <= lMax_; l++) {
232			for (int m = -l; m <= l; m++) {
233			q[std::make_pair(l,m)] = 0.0;
234			}
235			}
236			pos = sd->getPos();
237			rCOM = CenterOfMass - pos;
238			if (usePeriodicBoundaryConditions_)
239			currentSnapshot_->wrapVector(rCOM);
240			distCOM = rCOM.length();
241
242			// inner loop is over all other atoms in the system:
243
244			for (mol = info_->beginMolecule(mi); mol != NULL;
245			mol = info_->nextMolecule(mi)) {
246			for (atom = mol->beginAtom(ai); atom != NULL;
247			atom = mol->nextAtom(ai)) {
248
249			if (atom->getGlobalIndex() != myIndex) {
250			vec = pos - atom->getPos();
251
252			if (usePeriodicBoundaryConditions_)
253			currentSnapshot_->wrapVector(vec);
254
255			// Calculate "bonds" and build Q_lm(r) where
256			// Q_lm = Y_lm(theta(r),phi(r))
257			// The spherical harmonics are wrt any arbitrary coordinate
258			// system, we choose standard spherical coordinates
259
260			r = vec.length();
261
262			// Check to see if neighbor is in bond cutoff
263
264			if (r < rCut_) {
265			costheta = vec.z() / r;
266			phi = atan2(vec.y(), vec.x());
267
268			for (int l = 0; l <= lMax_; l++) {
269			sphericalHarmonic.setL(l);
270			for(int m = -l; m <= l; m++){
271			sphericalHarmonic.setM(m);
272			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
273			}
274			}
275			nBonds++;
276			}
277			}
278			}
279			}
280
281
282			for (int l = 0; l <= lMax_; l++) {
283			q2[l] = 0.0;
284			for (int m = -l; m <= l; m++){
285			q[std::make_pair(l,m)] /= (RealType)nBonds;
286			q2[l] += norm(q[std::make_pair(l,m)]);
287			}
288			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
289			}
290
291			// Find Third Order Invariant W_l
292
293			for (int l = 0; l <= lMax_; l++) {
294			w[l] = 0.0;
295			for (int m1 = -l; m1 <= l; m1++) {
296			std::pair<int,int> lm = std::make_pair(l, m1);
297			for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
298			int m2 = m2Min[lm] + mmm;
299			int m3 = -m1-m2;
300			w[l] += w3j[lm][mmm] * q[lm] *
301			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
302			}
303			}
304
305	gezelter	1782	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
306	chuckv	1128	}
307
308			collectHistogram(q_l, w_hat, distCOM);
309	chuckv	1137
310	chuckv	1194	// 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]));
311	chuckv	1137
312	chuckv	1128	}
313			}
314
315			writeOrderParameter();
316			}
317
318			void BOPofR::collectHistogram(std::vector<RealType> q,
319			std::vector<ComplexType> what, RealType distCOM) {
320
321			if ( distCOM < len_){
322			// Figure out where this distance goes...
323	gezelter	1790	int whichBin = int(distCOM / deltaR_);
324	chuckv	1137	RCount_[whichBin]++;
325
326			if(real(what[6]) < -0.15){
327			WofR_[whichBin]++;
328	chuckv	1128	}
329	chuckv	1137	if(q[6] > 0.5){
330			QofR_[whichBin]++;
331			}
332	chuckv	1128	}
333
334			}
335
336			void BOPofR::writeOrderParameter() {
337
338			std::ofstream osq((getOutputFileName() + "qr").c_str());
339
340			if (osq.is_open()) {
341
342			// Normalize by number of frames and write it out:
343
344			for (int i = 0; i < nBins_; ++i) {
345			RealType Rval = (i + 0.5) * deltaR_;
346			osq << Rval;
347	chuckv	1137	if (RCount_[i] == 0){
348			osq << "\t" << 0;
349			osq << "\n";
350			}else{
351			osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i];
352			osq << "\n";
353			}
354	chuckv	1128	}
355
356			osq.close();
357
358			} else {
359			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
360			(getOutputFileName() + "q").c_str());
361			painCave.isFatal = 1;
362			simError();
363			}
364
365			std::ofstream osw((getOutputFileName() + "wr").c_str());
366
367			if (osw.is_open()) {
368			// Normalize by number of frames and write it out:
369			for (int i = 0; i < nBins_; ++i) {
370			RealType Rval = deltaR_ * (i + 0.5);
371			osw << Rval;
372	chuckv	1137	if (RCount_[i] == 0){
373			osw << "\t" << 0;
374			osw << "\n";
375			}else{
376			osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i];
377			osw << "\n";
378			}
379	chuckv	1128	}
380
381			osw.close();
382			} else {
383			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
384			(getOutputFileName() + "w").c_str());
385			painCave.isFatal = 1;
386			simError();
387
388			}
389
390			}
391			}