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. 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, 24107 (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/BondOrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "math/Wigner3jm.hpp"

using namespace MATPACK;
namespace OpenMD {

  BondOrderParameter::BondOrderParameter(SimInfo* info, 
                                         const std::string& filename, 
                                         const std::string& sele,
                                         double rCut, 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:

    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_ = -1.1;
    MaxW_ = 1.1;
    deltaW_ = (MaxW_ - MinW_) / nbins;

    // 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;
  }
  
  BondOrderParameter::~BondOrderParameter() {
    Q_histogram_.clear();
    W_histogram_.clear();
    for (int l = 0; l <= lMax_; l++) {
      for (int m = -l; m <= l; m++) {
        w3j[std::make_pair(l,m)].clear();
      }
    }
    w3j.clear();
    m2Min.clear();
    m2Max.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;
    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;

    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();
      
      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();       

              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);
        
        Nbonds += nBonds;
        for (int l = 0; l <= lMax_;  l++) {
          for (int m = -l; m <= l; m++) {
            QBar[std::make_pair(l,m)] += (RealType)nBonds*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;
      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] * QBar[lm] * 
            QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
        }
      }
      
      W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
    }
    
    writeOrderParameter(Q, W_hat);    
  }

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

    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 = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();  
      }
    }

    for (int l = 0; l <= lMax_; l++) {
      if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
        int wbin = (real(what[l]) - MinW_) / deltaW_;
        W_histogram_[std::make_pair(wbin,l)] += 1;
        Wcount_[l]++;      
      } else {
        sprintf( painCave.errMsg,
                 "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();  
      }
    }

  }  


  void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, 
                                               std::vector<ComplexType> What) {
    
    std::ofstream osq((getOutputFileName() + "q").c_str());

    if (osq.is_open()) {
      
      osq << "# Bond Order Parameters\n";
      osq << "# selection: (" << selectionScript_ << ")\n";
      osq << "# \n";
      for (int l = 0; l <= lMax_; l++) {
        osq << "# <Q_" << l << ">: " << Q[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_;               
        osq << Qval;
        for (int l = 0; l <= lMax_; l++) {

          osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
        }
        osq << "\n";
      }

      osq.close();

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

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

    if (osw.is_open()) {
      osw << "# Bond Order Parameters\n";
      osw << "# selection: (" << selectionScript_ << ")\n";
      osw << "# \n";
      for (int l = 0; l <= lMax_; l++) {
        osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
      }
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Wval = MinW_ + (i + 0.5) * deltaW_;               
        osw << Wval;
        for (int l = 0; l <= lMax_; l++) {

          osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
        }
        osw << "\n";
      }

      osw.close();
    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              (getOutputFileName() + "w").c_str());
      painCave.isFatal = 1;
      simError();  
    }
       
  }
}
Revision:	1767
Committed:	Fri Jul 6 22:01:58 2012 UTC (12 years, 9 months ago) by gezelter
File size:	13889 byte(s)
Log Message:	Various fixes required to compile OpenMD with the MS Visual C++ compiler
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1038	* 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	1038	* 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	gezelter	1054	*
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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	gezelter	1054	* Created by J. Daniel Gezelter on 09/26/06.
42			* @author J. Daniel Gezelter
43	gezelter	1442	* @version $Id$
44	gezelter	1054	*
45	chuckv	1038	*/
46	gezelter	1039
47	chuckv	1038	#include "applications/staticProps/BondOrderParameter.hpp"
48			#include "utils/simError.h"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51			#include "utils/NumericConstant.hpp"
52	gezelter	1600	#include "math/Wigner3jm.hpp"
53	gezelter	1041
54	gezelter	1600	using namespace MATPACK;
55	gezelter	1390	namespace OpenMD {
56	chuckv	1038
57	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
58			const std::string& filename,
59			const std::string& sele,
60	gezelter	1052	double rCut, 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	chuckv	1038	rCut_ = rCut;
72	gezelter	1051	nBins_ = nbins;
73			Qcount_.resize(lMax_+1);
74			Wcount_.resize(lMax_+1);
75	gezelter	1048
76			// Q can take values from 0 to 1
77
78			MinQ_ = 0.0;
79	gezelter	1051	MaxQ_ = 1.1;
80	gezelter	1048	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81
82			// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
83			// use values for MinW_ and MaxW_ that are slightly larger than this:
84
85	gezelter	1100	MinW_ = -1.1;
86			MaxW_ = 1.1;
87	gezelter	1048	deltaW_ = (MaxW_ - MinW_) / nbins;
88	gezelter	1053
89			// Make arrays for Wigner3jm
90	gezelter	1600	RealType* THRCOF = new RealType[2*lMax_+1];
91	gezelter	1053	// Variables for Wigner routine
92	gezelter	1600	RealType lPass, m1Pass, m2m, m2M;
93	gezelter	1053	int error, mSize;
94			mSize = 2*lMax_+1;
95
96			for (int l = 0; l <= lMax_; l++) {
97	gezelter	1600	lPass = (RealType)l;
98	gezelter	1053	for (int m1 = -l; m1 <= l; m1++) {
99	gezelter	1600	m1Pass = (RealType)m1;
100	gezelter	1053
101			std::pair<int,int> lm = std::make_pair(l, m1);
102
103			// Zero work array
104			for (int ii = 0; ii < 2*l + 1; ii++){
105			THRCOF[ii] = 0.0;
106			}
107	gezelter	1100
108	gezelter	1053	// Get Wigner coefficients
109	gezelter	1600	Wigner3jm(lPass, lPass, lPass,
110			m1Pass, m2m, m2M,
111			THRCOF, mSize, error);
112	gezelter	1053
113			m2Min[lm] = (int)floor(m2m);
114			m2Max[lm] = (int)floor(m2M);
115
116	gezelter	1100	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
117	gezelter	1053	w3j[lm].push_back(THRCOF[mmm]);
118			}
119			}
120			}
121	gezelter	1054	delete [] THRCOF;
122			THRCOF = NULL;
123	gezelter	1039	}
124	gezelter	1053
125	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
126	gezelter	1048	Q_histogram_.clear();
127			W_histogram_.clear();
128	gezelter	1054	for (int l = 0; l <= lMax_; l++) {
129			for (int m = -l; m <= l; m++) {
130			w3j[std::make_pair(l,m)].clear();
131			}
132			}
133			w3j.clear();
134			m2Min.clear();
135			m2Max.clear();
136	gezelter	1041	}
137	gezelter	1054
138	gezelter	1048	void BondOrderParameter::initalizeHistogram() {
139	gezelter	1051	for (int bin = 0; bin < nBins_; bin++) {
140			for (int l = 0; l <= lMax_; l++) {
141			Q_histogram_[std::make_pair(bin,l)] = 0;
142			W_histogram_[std::make_pair(bin,l)] = 0;
143			}
144			}
145	gezelter	1048	}
146
147	gezelter	1039	void BondOrderParameter::process() {
148			Molecule* mol;
149			Atom* atom;
150			RigidBody* rb;
151	gezelter	1043	int myIndex;
152	gezelter	1039	SimInfo::MoleculeIterator mi;
153			Molecule::RigidBodyIterator rbIter;
154			Molecule::AtomIterator ai;
155			StuntDouble* sd;
156	gezelter	1043	Vector3d vec;
157	gezelter	1042	RealType costheta;
158	gezelter	1039	RealType phi;
159			RealType r;
160	gezelter	1051	std::map<std::pair<int,int>,ComplexType> q;
161			std::vector<RealType> q_l;
162	gezelter	1052	std::vector<RealType> q2;
163			std::vector<ComplexType> w;
164			std::vector<ComplexType> w_hat;
165	gezelter	1051	std::map<std::pair<int,int>,ComplexType> QBar;
166			std::vector<RealType> Q2;
167			std::vector<RealType> Q;
168			std::vector<ComplexType> W;
169			std::vector<ComplexType> W_hat;
170	gezelter	1048	int nBonds, Nbonds;
171	gezelter	1042	SphericalHarmonic sphericalHarmonic;
172	gezelter	1767	int i;
173	gezelter	1043
174	gezelter	1039	DumpReader reader(info_, dumpFilename_);
175			int nFrames = reader.getNFrames();
176	gezelter	1041	frameCounter_ = 0;
177	chuckv	1038
178	gezelter	1051	q_l.resize(lMax_+1);
179	gezelter	1052	q2.resize(lMax_+1);
180			w.resize(lMax_+1);
181			w_hat.resize(lMax_+1);
182
183	gezelter	1051	Q2.resize(lMax_+1);
184			Q.resize(lMax_+1);
185			W.resize(lMax_+1);
186			W_hat.resize(lMax_+1);
187	gezelter	1094	Nbonds = 0;
188	gezelter	1051
189	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
190			reader.readFrame(istep);
191	gezelter	1041	frameCounter_++;
192	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
193
194			if (evaluator_.isDynamic()) {
195			seleMan_.setSelectionSet(evaluator_.evaluate());
196			}
197	chuckv	1038
198	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
199	chuckv	1038
200	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
201			mol = info_->nextMolecule(mi)) {
202			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
203			rb = mol->nextRigidBody(rbIter)) {
204			rb->updateAtoms();
205			}
206	gezelter	1048	}
207
208	gezelter	1039	// outer loop is over the selected StuntDoubles:
209	chuckv	1038
210	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
211			sd = seleMan_.nextSelected(i)) {
212	chuckv	1038
213	gezelter	1043	myIndex = sd->getGlobalIndex();
214	gezelter	1048	nBonds = 0;
215	gezelter	1051
216			for (int l = 0; l <= lMax_; l++) {
217			for (int m = -l; m <= l; m++) {
218			q[std::make_pair(l,m)] = 0.0;
219			}
220	gezelter	1048	}
221	gezelter	1039
222			// inner loop is over all other atoms in the system:
223
224			for (mol = info_->beginMolecule(mi); mol != NULL;
225			mol = info_->nextMolecule(mi)) {
226			for (atom = mol->beginAtom(ai); atom != NULL;
227			atom = mol->nextAtom(ai)) {
228	chuckv	1038
229	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
230	chuckv	1038
231	gezelter	1043	vec = sd->getPos() - atom->getPos();
232	gezelter	1078
233			if (usePeriodicBoundaryConditions_)
234			currentSnapshot_->wrapVector(vec);
235	gezelter	1042
236	gezelter	1043	// Calculate "bonds" and build Q_lm(r) where
237			// Q_lm = Y_lm(theta(r),phi(r))
238			// The spherical harmonics are wrt any arbitrary coordinate
239			// system, we choose standard spherical coordinates
240
241			r = vec.length();
242
243			// Check to see if neighbor is in bond cutoff
244
245			if (r < rCut_) {
246			costheta = vec.z() / r;
247			phi = atan2(vec.y(), vec.x());
248	gezelter	1051
249			for (int l = 0; l <= lMax_; l++) {
250			sphericalHarmonic.setL(l);
251			for(int m = -l; m <= l; m++){
252			sphericalHarmonic.setM(m);
253			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
254			}
255	gezelter	1043	}
256			nBonds++;
257			}
258			}
259	gezelter	1039	}
260			}
261	gezelter	1051
262
263	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
264			q2[l] = 0.0;
265			for (int m = -l; m <= l; m++){
266	gezelter	1601	q[std::make_pair(l,m)] /= (RealType)nBonds;
267	gezelter	1052	q2[l] += norm(q[std::make_pair(l,m)]);
268			}
269	gezelter	1094	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
270	gezelter	1052	}
271	gezelter	1094
272	gezelter	1052	// Find Third Order Invariant W_l
273
274			for (int l = 0; l <= lMax_; l++) {
275			w[l] = 0.0;
276			for (int m1 = -l; m1 <= l; m1++) {
277	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
278	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
279	gezelter	1053	int m2 = m2Min[lm] + mmm;
280			int m3 = -m1-m2;
281			w[l] += w3j[lm][mmm] * q[lm] *
282			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
283	gezelter	1052	}
284			}
285
286	gezelter	1668	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
287	gezelter	1052	}
288
289			collectHistogram(q_l, w_hat);
290
291	gezelter	1048	Nbonds += nBonds;
292	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
293			for (int m = -l; m <= l; m++) {
294	gezelter	1094	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
295	gezelter	1051	}
296	gezelter	1048	}
297			}
298	gezelter	1047	}
299	gezelter	1051
300	gezelter	1047	// Normalize Qbar2
301	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
302			for (int m = -l; m <= l; m++){
303			QBar[std::make_pair(l,m)] /= Nbonds;
304			}
305	gezelter	1039	}
306
307	gezelter	1047	// Find second order invariant Q_l
308	gezelter	1039
309	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
310			Q2[l] = 0.0;
311			for (int m = -l; m <= l; m++){
312			Q2[l] += norm(QBar[std::make_pair(l,m)]);
313			}
314			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
315	gezelter	1039	}
316	gezelter	1047
317			// Find Third Order Invariant W_l
318
319	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
320			W[l] = 0.0;
321			for (int m1 = -l; m1 <= l; m1++) {
322	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
323	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
324	gezelter	1053	int m2 = m2Min[lm] + mmm;
325			int m3 = -m1-m2;
326			W[l] += w3j[lm][mmm] * QBar[lm] *
327			QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
328	gezelter	1051	}
329	gezelter	1047	}
330	gezelter	1041
331	gezelter	1668	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
332	gezelter	1039	}
333	gezelter	1047
334	gezelter	1051	writeOrderParameter(Q, W_hat);
335	gezelter	1047	}
336	chuckv	1038
337	gezelter	1052	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
338			std::vector<ComplexType> what) {
339	chuckv	1038
340	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
341			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
342			int qbin = (q[l] - MinQ_) / deltaQ_;
343			Q_histogram_[std::make_pair(qbin,l)] += 1;
344			Qcount_[l]++;
345			} else {
346			sprintf( painCave.errMsg,
347			"q_l value outside reasonable range\n");
348	gezelter	1390	painCave.severity = OPENMD_ERROR;
349	gezelter	1051	painCave.isFatal = 1;
350			simError();
351			}
352	gezelter	1048	}
353
354	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
355			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
356			int wbin = (real(what[l]) - MinW_) / deltaW_;
357			W_histogram_[std::make_pair(wbin,l)] += 1;
358			Wcount_[l]++;
359			} else {
360			sprintf( painCave.errMsg,
361	gezelter	1094	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
362	gezelter	1390	painCave.severity = OPENMD_ERROR;
363	gezelter	1052	painCave.isFatal = 1;
364			simError();
365			}
366			}
367
368	gezelter	1048	}
369
370
371	gezelter	1052	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
372			std::vector<ComplexType> What) {
373	gezelter	1051
374	gezelter	1052	std::ofstream osq((getOutputFileName() + "q").c_str());
375
376			if (osq.is_open()) {
377	gezelter	1041
378	gezelter	1052	osq << "# Bond Order Parameters\n";
379			osq << "# selection: (" << selectionScript_ << ")\n";
380			osq << "# \n";
381	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
382	gezelter	1052	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
383	gezelter	1051	}
384	gezelter	1048	// Normalize by number of frames and write it out:
385	gezelter	1051	for (int i = 0; i < nBins_; ++i) {
386			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
387	gezelter	1052	osq << Qval;
388	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
389	gezelter	1094
390			osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
391	gezelter	1051	}
392	gezelter	1052	osq << "\n";
393	gezelter	1048	}
394
395	gezelter	1052	osq.close();
396	gezelter	1047
397	gezelter	1041	} else {
398			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
399	gezelter	1052	(getOutputFileName() + "q").c_str());
400	gezelter	1041	painCave.isFatal = 1;
401			simError();
402			}
403	gezelter	1052
404			std::ofstream osw((getOutputFileName() + "w").c_str());
405
406			if (osw.is_open()) {
407			osw << "# Bond Order Parameters\n";
408			osw << "# selection: (" << selectionScript_ << ")\n";
409			osw << "# \n";
410			for (int l = 0; l <= lMax_; l++) {
411	gezelter	1090	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
412	gezelter	1052	}
413			// Normalize by number of frames and write it out:
414			for (int i = 0; i < nBins_; ++i) {
415			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
416			osw << Wval;
417			for (int l = 0; l <= lMax_; l++) {
418	gezelter	1094
419			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
420	gezelter	1052	}
421			osw << "\n";
422			}
423
424			osw.close();
425			} else {
426			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
427			(getOutputFileName() + "w").c_str());
428			painCave.isFatal = 1;
429			simError();
430			}
431
432	gezelter	1041	}
433	gezelter	1039	}