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, 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/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), seleMan_(info),
      evaluator_(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::initializeHistogram() {
    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 = int((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 = int((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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 1 month ago) by gezelter
File size:	13916 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	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	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	1782	#include "math/Wigner3jm.hpp"
53	gezelter	1041
54	gezelter	1782	using namespace MATPACK;
55	gezelter	1390	namespace OpenMD {
56	gezelter	2071
57	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
58			const std::string& filename,
59			const std::string& sele,
60	gezelter	2071	double rCut, int nbins)
61			: StaticAnalyser(info, filename), selectionScript_(sele), seleMan_(info),
62			evaluator_(info) {
63	gezelter	1039
64	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
65	chuckv	1038
66	gezelter	1039	evaluator_.loadScriptString(sele);
67			if (!evaluator_.isDynamic()) {
68			seleMan_.setSelectionSet(evaluator_.evaluate());
69	chuckv	1038	}
70
71	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
72
73	chuckv	1038	rCut_ = rCut;
74	gezelter	1051	nBins_ = nbins;
75			Qcount_.resize(lMax_+1);
76			Wcount_.resize(lMax_+1);
77	gezelter	1048
78			// Q can take values from 0 to 1
79
80			MinQ_ = 0.0;
81	gezelter	1051	MaxQ_ = 1.1;
82	gezelter	1048	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
83
84			// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
85			// use values for MinW_ and MaxW_ that are slightly larger than this:
86
87	gezelter	1100	MinW_ = -1.1;
88			MaxW_ = 1.1;
89	gezelter	1048	deltaW_ = (MaxW_ - MinW_) / nbins;
90	gezelter	1053
91			// Make arrays for Wigner3jm
92	gezelter	1782	RealType* THRCOF = new RealType[2*lMax_+1];
93	gezelter	1053	// Variables for Wigner routine
94	gezelter	1782	RealType lPass, m1Pass, m2m, m2M;
95	gezelter	1053	int error, mSize;
96			mSize = 2*lMax_+1;
97
98			for (int l = 0; l <= lMax_; l++) {
99	gezelter	1782	lPass = (RealType)l;
100	gezelter	1053	for (int m1 = -l; m1 <= l; m1++) {
101	gezelter	1782	m1Pass = (RealType)m1;
102	gezelter	1053
103			std::pair<int,int> lm = std::make_pair(l, m1);
104
105			// Zero work array
106			for (int ii = 0; ii < 2*l + 1; ii++){
107			THRCOF[ii] = 0.0;
108			}
109	gezelter	1100
110	gezelter	1053	// Get Wigner coefficients
111	gezelter	1782	Wigner3jm(lPass, lPass, lPass,
112			m1Pass, m2m, m2M,
113			THRCOF, mSize, error);
114	gezelter	1610
115	gezelter	1053	m2Min[lm] = (int)floor(m2m);
116			m2Max[lm] = (int)floor(m2M);
117
118	gezelter	1100	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
119	gezelter	1053	w3j[lm].push_back(THRCOF[mmm]);
120			}
121			}
122			}
123	gezelter	1054	delete [] THRCOF;
124			THRCOF = NULL;
125	gezelter	1039	}
126	gezelter	1053
127	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
128	gezelter	1048	Q_histogram_.clear();
129			W_histogram_.clear();
130	gezelter	1054	for (int l = 0; l <= lMax_; l++) {
131			for (int m = -l; m <= l; m++) {
132			w3j[std::make_pair(l,m)].clear();
133			}
134			}
135			w3j.clear();
136			m2Min.clear();
137			m2Max.clear();
138	gezelter	1041	}
139	gezelter	1054
140	jmichalk	1785	void BondOrderParameter::initializeHistogram() {
141	gezelter	1051	for (int bin = 0; bin < nBins_; bin++) {
142			for (int l = 0; l <= lMax_; l++) {
143			Q_histogram_[std::make_pair(bin,l)] = 0;
144			W_histogram_[std::make_pair(bin,l)] = 0;
145			}
146			}
147	gezelter	1048	}
148
149	gezelter	1039	void BondOrderParameter::process() {
150			Molecule* mol;
151			Atom* atom;
152			RigidBody* rb;
153	gezelter	1043	int myIndex;
154	gezelter	1039	SimInfo::MoleculeIterator mi;
155			Molecule::RigidBodyIterator rbIter;
156			Molecule::AtomIterator ai;
157			StuntDouble* sd;
158	gezelter	1043	Vector3d vec;
159	gezelter	1042	RealType costheta;
160	gezelter	1039	RealType phi;
161			RealType r;
162	gezelter	1051	std::map<std::pair<int,int>,ComplexType> q;
163			std::vector<RealType> q_l;
164	gezelter	1052	std::vector<RealType> q2;
165			std::vector<ComplexType> w;
166			std::vector<ComplexType> w_hat;
167	gezelter	1051	std::map<std::pair<int,int>,ComplexType> QBar;
168			std::vector<RealType> Q2;
169			std::vector<RealType> Q;
170			std::vector<ComplexType> W;
171			std::vector<ComplexType> W_hat;
172	gezelter	1048	int nBonds, Nbonds;
173	gezelter	1042	SphericalHarmonic sphericalHarmonic;
174	gezelter	1782	int i;
175	gezelter	1043
176	gezelter	1039	DumpReader reader(info_, dumpFilename_);
177			int nFrames = reader.getNFrames();
178	gezelter	1041	frameCounter_ = 0;
179	chuckv	1038
180	gezelter	1051	q_l.resize(lMax_+1);
181	gezelter	1052	q2.resize(lMax_+1);
182			w.resize(lMax_+1);
183			w_hat.resize(lMax_+1);
184
185	gezelter	1051	Q2.resize(lMax_+1);
186			Q.resize(lMax_+1);
187			W.resize(lMax_+1);
188			W_hat.resize(lMax_+1);
189	gezelter	1094	Nbonds = 0;
190	gezelter	1051
191	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
192			reader.readFrame(istep);
193	gezelter	1041	frameCounter_++;
194	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
195
196			if (evaluator_.isDynamic()) {
197			seleMan_.setSelectionSet(evaluator_.evaluate());
198			}
199	chuckv	1038
200	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
201	chuckv	1038
202	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
203			mol = info_->nextMolecule(mi)) {
204			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
205			rb = mol->nextRigidBody(rbIter)) {
206			rb->updateAtoms();
207			}
208	gezelter	1048	}
209
210	gezelter	1039	// outer loop is over the selected StuntDoubles:
211	chuckv	1038
212	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
213			sd = seleMan_.nextSelected(i)) {
214	chuckv	1038
215	gezelter	1043	myIndex = sd->getGlobalIndex();
216	gezelter	1048	nBonds = 0;
217	gezelter	1051
218			for (int l = 0; l <= lMax_; l++) {
219			for (int m = -l; m <= l; m++) {
220			q[std::make_pair(l,m)] = 0.0;
221			}
222	gezelter	1048	}
223	gezelter	1039
224			// inner loop is over all other atoms in the system:
225
226			for (mol = info_->beginMolecule(mi); mol != NULL;
227			mol = info_->nextMolecule(mi)) {
228			for (atom = mol->beginAtom(ai); atom != NULL;
229			atom = mol->nextAtom(ai)) {
230	chuckv	1038
231	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
232	chuckv	1038
233	gezelter	1043	vec = sd->getPos() - atom->getPos();
234	gezelter	1078
235			if (usePeriodicBoundaryConditions_)
236			currentSnapshot_->wrapVector(vec);
237	gezelter	1042
238	gezelter	1043	// Calculate "bonds" and build Q_lm(r) where
239			// Q_lm = Y_lm(theta(r),phi(r))
240			// The spherical harmonics are wrt any arbitrary coordinate
241			// system, we choose standard spherical coordinates
242
243			r = vec.length();
244
245			// Check to see if neighbor is in bond cutoff
246
247			if (r < rCut_) {
248			costheta = vec.z() / r;
249			phi = atan2(vec.y(), vec.x());
250	gezelter	1051
251			for (int l = 0; l <= lMax_; l++) {
252			sphericalHarmonic.setL(l);
253			for(int m = -l; m <= l; m++){
254			sphericalHarmonic.setM(m);
255			q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256	gezelter	1610
257	gezelter	1051	}
258	gezelter	1043	}
259			nBonds++;
260			}
261			}
262	gezelter	1039	}
263			}
264	gezelter	1051
265
266	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
267			q2[l] = 0.0;
268			for (int m = -l; m <= l; m++){
269	gezelter	1782	q[std::make_pair(l,m)] /= (RealType)nBonds;
270	gezelter	1610
271	gezelter	1052	q2[l] += norm(q[std::make_pair(l,m)]);
272			}
273	gezelter	1094	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
274	gezelter	1052	}
275	gezelter	1094
276	gezelter	1052	// Find Third Order Invariant W_l
277
278			for (int l = 0; l <= lMax_; l++) {
279			w[l] = 0.0;
280			for (int m1 = -l; m1 <= l; m1++) {
281	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
282	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
283	gezelter	1053	int m2 = m2Min[lm] + mmm;
284			int m3 = -m1-m2;
285			w[l] += w3j[lm][mmm] * q[lm] *
286			q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)];
287	gezelter	1052	}
288			}
289
290	gezelter	1782	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
291	gezelter	1052	}
292
293			collectHistogram(q_l, w_hat);
294
295	gezelter	1048	Nbonds += nBonds;
296	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
297			for (int m = -l; m <= l; m++) {
298	gezelter	1094	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
299	gezelter	1051	}
300	gezelter	1048	}
301			}
302	gezelter	1047	}
303	gezelter	1051
304	gezelter	1047	// Normalize Qbar2
305	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
306			for (int m = -l; m <= l; m++){
307			QBar[std::make_pair(l,m)] /= Nbonds;
308			}
309	gezelter	1039	}
310
311	gezelter	1047	// Find second order invariant Q_l
312	gezelter	1039
313	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
314			Q2[l] = 0.0;
315			for (int m = -l; m <= l; m++){
316			Q2[l] += norm(QBar[std::make_pair(l,m)]);
317			}
318			Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
319	gezelter	1039	}
320	gezelter	1047
321			// Find Third Order Invariant W_l
322
323	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
324			W[l] = 0.0;
325			for (int m1 = -l; m1 <= l; m1++) {
326	gezelter	1053	std::pair<int,int> lm = std::make_pair(l, m1);
327	gezelter	1100	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
328	gezelter	1053	int m2 = m2Min[lm] + mmm;
329			int m3 = -m1-m2;
330			W[l] += w3j[lm][mmm] * QBar[lm] *
331			QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
332	gezelter	1051	}
333	gezelter	1047	}
334	gezelter	1041
335	gezelter	1782	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
336	gezelter	1039	}
337	gezelter	1047
338	gezelter	1051	writeOrderParameter(Q, W_hat);
339	gezelter	1047	}
340	chuckv	1038
341	gezelter	1052	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
342			std::vector<ComplexType> what) {
343	chuckv	1038
344	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
345			if (q[l] >= MinQ_ && q[l] < MaxQ_) {
346	gezelter	1790	int qbin = int((q[l] - MinQ_) / deltaQ_);
347	gezelter	1051	Q_histogram_[std::make_pair(qbin,l)] += 1;
348			Qcount_[l]++;
349			} else {
350			sprintf( painCave.errMsg,
351			"q_l value outside reasonable range\n");
352	gezelter	1390	painCave.severity = OPENMD_ERROR;
353	gezelter	1051	painCave.isFatal = 1;
354			simError();
355			}
356	gezelter	1048	}
357
358	gezelter	1052	for (int l = 0; l <= lMax_; l++) {
359			if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
360	gezelter	1790	int wbin = int((real(what[l]) - MinW_) / deltaW_);
361	gezelter	1052	W_histogram_[std::make_pair(wbin,l)] += 1;
362			Wcount_[l]++;
363			} else {
364			sprintf( painCave.errMsg,
365	gezelter	1094	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
366	gezelter	1390	painCave.severity = OPENMD_ERROR;
367	gezelter	1052	painCave.isFatal = 1;
368			simError();
369			}
370			}
371
372	gezelter	1048	}
373
374
375	gezelter	1052	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
376			std::vector<ComplexType> What) {
377	gezelter	1051
378	gezelter	1052	std::ofstream osq((getOutputFileName() + "q").c_str());
379
380			if (osq.is_open()) {
381	gezelter	1041
382	gezelter	1052	osq << "# Bond Order Parameters\n";
383			osq << "# selection: (" << selectionScript_ << ")\n";
384			osq << "# \n";
385	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
386	gezelter	1052	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
387	gezelter	1051	}
388	gezelter	1048	// Normalize by number of frames and write it out:
389	gezelter	1051	for (int i = 0; i < nBins_; ++i) {
390			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
391	gezelter	1052	osq << Qval;
392	gezelter	1051	for (int l = 0; l <= lMax_; l++) {
393	gezelter	1094
394			osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
395	gezelter	1051	}
396	gezelter	1052	osq << "\n";
397	gezelter	1048	}
398
399	gezelter	1052	osq.close();
400	gezelter	1047
401	gezelter	1041	} else {
402			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
403	gezelter	1052	(getOutputFileName() + "q").c_str());
404	gezelter	1041	painCave.isFatal = 1;
405			simError();
406			}
407	gezelter	1052
408			std::ofstream osw((getOutputFileName() + "w").c_str());
409
410			if (osw.is_open()) {
411			osw << "# Bond Order Parameters\n";
412			osw << "# selection: (" << selectionScript_ << ")\n";
413			osw << "# \n";
414			for (int l = 0; l <= lMax_; l++) {
415	gezelter	1090	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
416	gezelter	1052	}
417			// Normalize by number of frames and write it out:
418			for (int i = 0; i < nBins_; ++i) {
419			RealType Wval = MinW_ + (i + 0.5) * deltaW_;
420			osw << Wval;
421			for (int l = 0; l <= lMax_; l++) {
422	gezelter	1094
423			osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
424	gezelter	1052	}
425			osw << "\n";
426			}
427
428			osw.close();
429			} else {
430			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
431			(getOutputFileName() + "w").c_str());
432			painCave.isFatal = 1;
433			simError();
434			}
435
436	gezelter	1041	}
437	gezelter	1039	}