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();    
  }
  

  IcosahedralOfR::IcosahedralOfR(SimInfo* info, const std::string& filename, 
                                 const std::string& sele, double rCut, 
                                 int nbins, RealType len) : BOPofR(info, 
                                                                   filename, 
                                                                   sele, rCut,
                                                                   nbins, len) {
  }

  void IcosahedralOfR::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]++;
      }
    }      
  }

  FCCOfR::FCCOfR(SimInfo* info, const std::string& filename, 
                 const std::string& sele, double rCut, 
                 int nbins, RealType len) : BOPofR(info, filename, sele, rCut,
                                                   nbins, len) {}
  
  
  void FCCOfR::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[4]) < -0.12){                                
        WofR_[whichBin]++;
      }
    }      
  }
  
  void IcosahedralOfR::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();  
    
    }
        
  }
  void FCCOfR::writeOrderParameter() {
    
    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:	1992
Committed:	Thu Apr 24 17:30:00 2014 UTC (11 years ago) by gezelter
File size:	13843 byte(s)
Log Message:	Added FCCOfR and IcosahedralOfR analyzers to staticProps
#	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	gezelter	1992	BOPofR::BOPofR(SimInfo* info, const std::string& filename,
59			const std::string& sele, double rCut, int nbins,
60			RealType len) : StaticAnalyser(info, filename),
61			selectionScript_(sele),
62			evaluator_(info), seleMan_(info) {
63	chuckv	1128
64			setOutputName(getPrefix(filename) + ".bo");
65	gezelter	1992
66	chuckv	1128	evaluator_.loadScriptString(sele);
67			if (!evaluator_.isDynamic()) {
68			seleMan_.setSelectionSet(evaluator_.evaluate());
69			}
70	gezelter	1992
71	chuckv	1128	// Set up cutoff radius and order of the Legendre Polynomial:
72	gezelter	1992
73	chuckv	1128	rCut_ = rCut;
74			nBins_ = nbins;
75			len_ = len;
76	gezelter	1992
77	chuckv	1128	deltaR_ = len_/nBins_;
78			RCount_.resize(nBins_);
79			WofR_.resize(nBins_);
80			QofR_.resize(nBins_);
81	chuckv	1137
82	gezelter	1992	for (int i = 0; i < nBins_; i++){
83			RCount_[i] = 0;
84			WofR_[i] = 0;
85			QofR_[i] = 0;
86			}
87
88	chuckv	1128	// Make arrays for Wigner3jm
89	gezelter	1782	RealType* THRCOF = new RealType[2*lMax_+1];
90	chuckv	1128	// Variables for Wigner routine
91	gezelter	1782	RealType lPass, m1Pass, m2m, m2M;
92	chuckv	1128	int error, mSize;
93			mSize = 2*lMax_+1;
94
95			for (int l = 0; l <= lMax_; l++) {
96	gezelter	1782	lPass = (RealType)l;
97	chuckv	1128	for (int m1 = -l; m1 <= l; m1++) {
98	gezelter	1782	m1Pass = (RealType)m1;
99	chuckv	1128
100			std::pair<int,int> lm = std::make_pair(l, m1);
101
102			// Zero work array
103			for (int ii = 0; ii < 2*l + 1; ii++){
104			THRCOF[ii] = 0.0;
105			}
106
107			// Get Wigner coefficients
108	gezelter	1782	Wigner3jm(lPass, lPass, lPass,
109			m1Pass, m2m, m2M,
110			THRCOF, mSize, error);
111	chuckv	1128
112			m2Min[lm] = (int)floor(m2m);
113			m2Max[lm] = (int)floor(m2M);
114
115			for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
116			w3j[lm].push_back(THRCOF[mmm]);
117			}
118			}
119			}
120
121			delete [] THRCOF;
122	chuckv	1137	THRCOF = NULL;
123	chuckv	1128
124			}
125
126			BOPofR::~BOPofR() {
127	gezelter	1992	/*
128			std::cerr << "Freeing stuff" << std::endl;
129	chuckv	1128	for (int l = 0; l <= lMax_; l++) {
130			for (int m = -l; m <= l; m++) {
131			w3j[std::make_pair(l,m)].clear();
132			}
133			}
134			std::cerr << "w3j made free...." << std::endl;
135			for (int bin = 0; bin < nBins_; bin++) {
136			QofR_[bin].clear();
137			WofR_[bin].clear();
138			RCount_[bin].clear();
139			}
140			std::cout << "R arrays made free...." << std::endl;
141			w3j.clear();
142			m2Min.clear();
143			m2Max.clear();
144			RCount_.clear();
145			WofR_.clear();
146			QofR_.clear();
147			*/
148			}
149
150
151	jmichalk	1785	void BOPofR::initializeHistogram() {
152	gezelter	1992	for (int i = 0; i < nBins_; i++){
153			RCount_[i] = 0;
154			WofR_[i] = 0;
155			QofR_[i] = 0;
156			}
157	chuckv	1128	}
158	gezelter	1992
159
160	chuckv	1128	void BOPofR::process() {
161			Molecule* mol;
162			Atom* atom;
163			RigidBody* rb;
164			int myIndex;
165			SimInfo::MoleculeIterator mi;
166			Molecule::RigidBodyIterator rbIter;
167			Molecule::AtomIterator ai;
168			StuntDouble* sd;
169			Vector3d vec;
170			RealType costheta;
171			RealType phi;
172			RealType r;
173			Vector3d rCOM;
174			RealType distCOM;
175			Vector3d pos;
176			Vector3d CenterOfMass;
177			std::map<std::pair<int,int>,ComplexType> q;
178			std::vector<RealType> q_l;
179			std::vector<RealType> q2;
180			std::vector<ComplexType> w;
181			std::vector<ComplexType> w_hat;
182			std::vector<RealType> Q2;
183			std::vector<RealType> Q;
184			std::vector<ComplexType> W;
185			std::vector<ComplexType> W_hat;
186	gezelter	1793	int nBonds;
187	chuckv	1128	SphericalHarmonic sphericalHarmonic;
188	gezelter	1782	int i;
189
190	chuckv	1128	DumpReader reader(info_, dumpFilename_);
191			int nFrames = reader.getNFrames();
192			frameCounter_ = 0;
193
194	gezelter	1782	Thermo thermo(info_);
195
196	chuckv	1128	q_l.resize(lMax_+1);
197			q2.resize(lMax_+1);
198			w.resize(lMax_+1);
199			w_hat.resize(lMax_+1);
200
201			Q2.resize(lMax_+1);
202			Q.resize(lMax_+1);
203			W.resize(lMax_+1);
204			W_hat.resize(lMax_+1);
205
206			for (int istep = 0; istep < nFrames; istep += step_) {
207			reader.readFrame(istep);
208			frameCounter_++;
209			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
210	gezelter	1782	CenterOfMass = thermo.getCom();
211	chuckv	1128	if (evaluator_.isDynamic()) {
212			seleMan_.setSelectionSet(evaluator_.evaluate());
213			}
214
215			// update the positions of atoms which belong to the rigidbodies
216
217			for (mol = info_->beginMolecule(mi); mol != NULL;
218			mol = info_->nextMolecule(mi)) {
219			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
220			rb = mol->nextRigidBody(rbIter)) {
221			rb->updateAtoms();
222			}
223			}
224
225			// outer loop is over the selected StuntDoubles:
226
227			for (sd = seleMan_.beginSelected(i); sd != NULL;
228			sd = seleMan_.nextSelected(i)) {
229
230			myIndex = sd->getGlobalIndex();
231
232			nBonds = 0;
233
234			for (int l = 0; l <= lMax_; l++) {
235			for (int m = -l; m <= l; m++) {
236			q[std::make_pair(l,m)] = 0.0;
237			}
238			}
239			pos = sd->getPos();
240			rCOM = CenterOfMass - pos;
241			if (usePeriodicBoundaryConditions_)
242			currentSnapshot_->wrapVector(rCOM);
243			distCOM = rCOM.length();
244
245			// inner loop is over all other atoms in the system:
246
247			for (mol = info_->beginMolecule(mi); mol != NULL;
248			mol = info_->nextMolecule(mi)) {
249			for (atom = mol->beginAtom(ai); atom != NULL;
250			atom = mol->nextAtom(ai)) {
251
252			if (atom->getGlobalIndex() != myIndex) {
253			vec = pos - atom->getPos();
254
255			if (usePeriodicBoundaryConditions_)
256			currentSnapshot_->wrapVector(vec);
257
258			// Calculate "bonds" and build Q_lm(r) where
259			// Q_lm = Y_lm(theta(r),phi(r))
260			// The spherical harmonics are wrt any arbitrary coordinate
261			// system, we choose standard spherical coordinates
262
263			r = vec.length();
264
265			// Check to see if neighbor is in bond cutoff
266
267			if (r < rCut_) {
268			costheta = vec.z() / r;
269			phi = atan2(vec.y(), vec.x());
270
271			for (int l = 0; l <= lMax_; l++) {
272			sphericalHarmonic.setL(l);
273			for(int m = -l; m <= l; m++){
274			sphericalHarmonic.setM(m);
275			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
276			}
277			}
278			nBonds++;
279			}
280			}
281			}
282			}
283
284
285			for (int l = 0; l <= lMax_; l++) {
286			q2[l] = 0.0;
287			for (int m = -l; m <= l; m++){
288			q[std::make_pair(l,m)] /= (RealType)nBonds;
289			q2[l] += norm(q[std::make_pair(l,m)]);
290			}
291			q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
292			}
293
294			// Find Third Order Invariant W_l
295
296			for (int l = 0; l <= lMax_; l++) {
297			w[l] = 0.0;
298			for (int m1 = -l; m1 <= l; m1++) {
299			std::pair<int,int> lm = std::make_pair(l, m1);
300			for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
301			int m2 = m2Min[lm] + mmm;
302			int m3 = -m1-m2;
303			w[l] += w3j[lm][mmm] * q[lm] *
304			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
305			}
306			}
307
308	gezelter	1782	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
309	chuckv	1128	}
310
311			collectHistogram(q_l, w_hat, distCOM);
312	chuckv	1137
313	gezelter	1992	// 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]));
314
315	chuckv	1128	}
316			}
317	gezelter	1992
318	chuckv	1128	writeOrderParameter();
319			}
320	gezelter	1992
321	chuckv	1128
322
323	gezelter	1992	IcosahedralOfR::IcosahedralOfR(SimInfo* info, const std::string& filename,
324			const std::string& sele, double rCut,
325			int nbins, RealType len) : BOPofR(info,
326			filename,
327			sele, rCut,
328			nbins, len) {
329			}
330
331			void IcosahedralOfR::collectHistogram(std::vector<RealType> q,
332			std::vector<ComplexType> what,
333			RealType distCOM) {
334
335	chuckv	1128	if ( distCOM < len_){
336			// Figure out where this distance goes...
337	gezelter	1790	int whichBin = int(distCOM / deltaR_);
338	chuckv	1137	RCount_[whichBin]++;
339
340			if(real(what[6]) < -0.15){
341	gezelter	1992	WofR_[whichBin]++;
342	chuckv	1128	}
343	gezelter	1992	if(q[6] > 0.5){
344	chuckv	1137	QofR_[whichBin]++;
345	gezelter	1992	}
346			}
347	chuckv	1128	}
348
349	gezelter	1992	FCCOfR::FCCOfR(SimInfo* info, const std::string& filename,
350			const std::string& sele, double rCut,
351			int nbins, RealType len) : BOPofR(info, filename, sele, rCut,
352			nbins, len) {}
353
354
355			void FCCOfR::collectHistogram(std::vector<RealType> q,
356			std::vector<ComplexType> what,
357			RealType distCOM) {
358	chuckv	1128
359	gezelter	1992	if ( distCOM < len_){
360			// Figure out where this distance goes...
361			int whichBin = int(distCOM / deltaR_);
362			RCount_[whichBin]++;
363
364			if(real(what[4]) < -0.12){
365			WofR_[whichBin]++;
366			}
367			}
368			}
369
370			void IcosahedralOfR::writeOrderParameter() {
371
372	chuckv	1128	std::ofstream osq((getOutputFileName() + "qr").c_str());
373
374			if (osq.is_open()) {
375
376			// Normalize by number of frames and write it out:
377	gezelter	1992
378	chuckv	1128	for (int i = 0; i < nBins_; ++i) {
379			RealType Rval = (i + 0.5) * deltaR_;
380			osq << Rval;
381	gezelter	1992	if (RCount_[i] == 0){
382			osq << "\t" << 0;
383			osq << "\n";
384			}else{
385			osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i];
386			osq << "\n";
387			}
388	chuckv	1128	}
389	gezelter	1992
390	chuckv	1128	osq.close();
391	gezelter	1992
392	chuckv	1128	} else {
393			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
394			(getOutputFileName() + "q").c_str());
395			painCave.isFatal = 1;
396			simError();
397			}
398	gezelter	1992
399	chuckv	1128	std::ofstream osw((getOutputFileName() + "wr").c_str());
400	gezelter	1992
401	chuckv	1128	if (osw.is_open()) {
402			// Normalize by number of frames and write it out:
403			for (int i = 0; i < nBins_; ++i) {
404			RealType Rval = deltaR_ * (i + 0.5);
405			osw << Rval;
406	gezelter	1992	if (RCount_[i] == 0){
407			osw << "\t" << 0;
408			osw << "\n";
409			}else{
410			osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i];
411			osw << "\n";
412			}
413	chuckv	1128	}
414	gezelter	1992
415	chuckv	1128	osw.close();
416			} else {
417			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
418			(getOutputFileName() + "w").c_str());
419			painCave.isFatal = 1;
420			simError();
421
422			}
423
424			}
425	gezelter	1992	void FCCOfR::writeOrderParameter() {
426
427			std::ofstream osw((getOutputFileName() + "wr").c_str());
428
429			if (osw.is_open()) {
430			// Normalize by number of frames and write it out:
431			for (int i = 0; i < nBins_; ++i) {
432			RealType Rval = deltaR_ * (i + 0.5);
433			osw << Rval;
434			if (RCount_[i] == 0){
435			osw << "\t" << 0;
436			osw << "\n";
437			}else{
438			osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i];
439			osw << "\n";
440			}
441			}
442
443			osw.close();
444			} else {
445			sprintf(painCave.errMsg, "BOPofR: unable to open %s\n",
446			(getOutputFileName() + "w").c_str());
447			painCave.isFatal = 1;
448			simError();
449
450			}
451
452			}
453	chuckv	1128	}