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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */


/* Creates orientational bond order parameters as outlined by
 *     Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
 *     Phys Rev B, 28,784,1983
 * 
 */
 
#include "applications/staticProps/BondOrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "math/SphericalHarmonic.hpp"

namespace oopse {

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

    lNumber_ = lNumber;
    rCut_ = rCut;
    mSize_ = 2*lNumber_+1;    
  }

  BondOrderParameter::~BondOrderParameter() {
  }

  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;
    RealType dist;
    std::map<int,ComplexType> QBar_lm;
    RealType QSq_l;
    RealType Q_l;
    ComplexType W_l;
    ComplexType W_l_hat;
    int nBonds;
    SphericalHarmonic sphericalHarmonic;
    int i, j;
    // Make arrays for Wigner3jm
    double* THRCOF = new double[mSize_];
    // Variables for Wigner routine
    double l_ = (double)lNumber_;
    double m1Pass, m2Min, m2Max;
    int error, m1, m2, m3;

    // Set the l for the spherical harmonic, it doesn't change
    sphericalHarmonic.setL(lNumber_);

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    frameCounter_ = 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();
        }        
      }      
      
      nBonds = 0;
      
      for (int m = -lNumber_; m <= lNumber_; m++) {
        QBar_lm[m] = 0.0;
      }
      
      // outer loop is over the selected StuntDoubles:

      for (sd = seleMan_.beginSelected(i); sd != NULL; 
           sd = seleMan_.nextSelected(i)) {

        myIndex = sd->getGlobalIndex();
        
        // 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();       
              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 m = -lNumber_; m <= lNumber_; m++){
                  sphericalHarmonic.setM(m);
                  QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
                }
                nBonds++;
              }  
            }
          }
        }
      }      
    }

    // Normalize Qbar2
    for (int m = -lNumber_;m <= lNumber_; m++){
      QBar_lm[m] /= nBonds;
    }
    
    // Find second order invariant Q_l
    
    QSq_l = 0.0;
    for (int m = -lNumber_; m <= lNumber_; m++){
      QSq_l += norm(QBar_lm[m]);
    }
    
    std::cout << "qsl = " << QSq_l << "\n";
    Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
    
    // Find Third Order Invariant W_l
    
    W_l = 0.0;
    for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
      // Zero work array
      for (int ii = 0; ii < mSize_; ii++){
        THRCOF[ii] = 0.0;
      }
      // Get Wigner coefficients
      m1Pass = (double)m1;
      
      Wigner3jm(&l_, &l_, &l_, 
                &m1Pass, &m2Min, &m2Max, 
                THRCOF, &mSize_, &error);
      
      for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
        m2 = (int)floor(m2Min) + mmm;
        m3 = -m1-m2;
        W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
      }
    }
    
    W_l_hat = W_l / pow(QSq_l, 1.5);               
    
    writeOrderParameter(Q_l, real(W_l_hat));    
  }


  void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {

    std::ofstream os(getOutputFileName().c_str());

    if (os.is_open()) {
      
      os << "# Bond Order Parameters\n";
      os << "# selection: (" << selectionScript_ << ")\n";
      os << "# \n";
      os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
      os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
      os.close();

    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();  
    }
  }
}
Revision:	1047
Committed:	Thu Sep 21 21:47:17 2006 UTC (18 years, 7 months ago) by gezelter
File size:	8192 byte(s)
Log Message:	more bug fixes
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42
43			/* Creates orientational bond order parameters as outlined by
44			* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
45			* Phys Rev B, 28,784,1983
46			*
47			*/
48	gezelter	1039
49	chuckv	1038	#include "applications/staticProps/BondOrderParameter.hpp"
50			#include "utils/simError.h"
51			#include "io/DumpReader.hpp"
52			#include "primitives/Molecule.hpp"
53			#include "utils/NumericConstant.hpp"
54	gezelter	1042	#include "math/SphericalHarmonic.hpp"
55	gezelter	1041
56	chuckv	1038	namespace oopse {
57
58	gezelter	1039	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	1041	double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	1039
63	gezelter	1041	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	1038
65	gezelter	1039	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	1038	}
69
70	gezelter	1039	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	1038	lNumber_ = lNumber;
73			rCut_ = rCut;
74	gezelter	1039	mSize_ = 2*lNumber_+1;
75			}
76	chuckv	1038
77	gezelter	1041	BondOrderParameter::~BondOrderParameter() {
78			}
79
80	gezelter	1039	void BondOrderParameter::process() {
81			Molecule* mol;
82			Atom* atom;
83			RigidBody* rb;
84	gezelter	1043	int myIndex;
85	gezelter	1039	SimInfo::MoleculeIterator mi;
86			Molecule::RigidBodyIterator rbIter;
87			Molecule::AtomIterator ai;
88			StuntDouble* sd;
89	gezelter	1043	Vector3d vec;
90	gezelter	1042	RealType costheta;
91	gezelter	1039	RealType phi;
92			RealType r;
93			RealType dist;
94	gezelter	1046	std::map<int,ComplexType> QBar_lm;
95	gezelter	1039	RealType QSq_l;
96			RealType Q_l;
97	gezelter	1043	ComplexType W_l;
98			ComplexType W_l_hat;
99	gezelter	1039	int nBonds;
100	gezelter	1042	SphericalHarmonic sphericalHarmonic;
101	gezelter	1039	int i, j;
102	gezelter	1043	// Make arrays for Wigner3jm
103			double* THRCOF = new double[mSize_];
104			// Variables for Wigner routine
105			double l_ = (double)lNumber_;
106			double m1Pass, m2Min, m2Max;
107			int error, m1, m2, m3;
108
109	gezelter	1040	// Set the l for the spherical harmonic, it doesn't change
110			sphericalHarmonic.setL(lNumber_);
111
112	gezelter	1039	DumpReader reader(info_, dumpFilename_);
113			int nFrames = reader.getNFrames();
114	gezelter	1041	frameCounter_ = 0;
115	chuckv	1038
116	gezelter	1039	for (int istep = 0; istep < nFrames; istep += step_) {
117			reader.readFrame(istep);
118	gezelter	1041	frameCounter_++;
119	gezelter	1039	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
120
121			if (evaluator_.isDynamic()) {
122			seleMan_.setSelectionSet(evaluator_.evaluate());
123			}
124	chuckv	1038
125	gezelter	1039	// update the positions of atoms which belong to the rigidbodies
126	chuckv	1038
127	gezelter	1039	for (mol = info_->beginMolecule(mi); mol != NULL;
128			mol = info_->nextMolecule(mi)) {
129			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
130			rb = mol->nextRigidBody(rbIter)) {
131			rb->updateAtoms();
132			}
133			}
134
135	gezelter	1047	nBonds = 0;
136
137			for (int m = -lNumber_; m <= lNumber_; m++) {
138			QBar_lm[m] = 0.0;
139			}
140
141	gezelter	1039	// outer loop is over the selected StuntDoubles:
142	chuckv	1038
143	gezelter	1039	for (sd = seleMan_.beginSelected(i); sd != NULL;
144			sd = seleMan_.nextSelected(i)) {
145	chuckv	1038
146	gezelter	1043	myIndex = sd->getGlobalIndex();
147	gezelter	1039
148			// inner loop is over all other atoms in the system:
149
150			for (mol = info_->beginMolecule(mi); mol != NULL;
151			mol = info_->nextMolecule(mi)) {
152			for (atom = mol->beginAtom(ai); atom != NULL;
153			atom = mol->nextAtom(ai)) {
154	chuckv	1038
155	gezelter	1043	if (atom->getGlobalIndex() != myIndex) {
156	chuckv	1038
157	gezelter	1043	vec = sd->getPos() - atom->getPos();
158			currentSnapshot_->wrapVector(vec);
159	gezelter	1042
160	gezelter	1043	// Calculate "bonds" and build Q_lm(r) where
161			// Q_lm = Y_lm(theta(r),phi(r))
162			// The spherical harmonics are wrt any arbitrary coordinate
163			// system, we choose standard spherical coordinates
164
165			r = vec.length();
166
167			// Check to see if neighbor is in bond cutoff
168
169			if (r < rCut_) {
170			costheta = vec.z() / r;
171			phi = atan2(vec.y(), vec.x());
172
173			for(int m = -lNumber_; m <= lNumber_; m++){
174			sphericalHarmonic.setM(m);
175	gezelter	1047	QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
176	gezelter	1043	}
177			nBonds++;
178			}
179			}
180	gezelter	1039	}
181			}
182	gezelter	1047	}
183			}
184	chuckv	1038
185	gezelter	1047	// Normalize Qbar2
186			for (int m = -lNumber_;m <= lNumber_; m++){
187			QBar_lm[m] /= nBonds;
188	gezelter	1039	}
189
190	gezelter	1047	// Find second order invariant Q_l
191	gezelter	1039
192	gezelter	1047	QSq_l = 0.0;
193			for (int m = -lNumber_; m <= lNumber_; m++){
194			QSq_l += norm(QBar_lm[m]);
195	gezelter	1039	}
196	gezelter	1047
197			std::cout << "qsl = " << QSq_l << "\n";
198			Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
199
200			// Find Third Order Invariant W_l
201
202			W_l = 0.0;
203			for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
204			// Zero work array
205			for (int ii = 0; ii < mSize_; ii++){
206			THRCOF[ii] = 0.0;
207			}
208			// Get Wigner coefficients
209			m1Pass = (double)m1;
210	gezelter	1041
211	gezelter	1047	Wigner3jm(&l_, &l_, &l_,
212			&m1Pass, &m2Min, &m2Max,
213			THRCOF, &mSize_, &error);
214	gezelter	1041
215	gezelter	1047	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
216			m2 = (int)floor(m2Min) + mmm;
217			m3 = -m1-m2;
218			W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
219	gezelter	1041	}
220	gezelter	1039	}
221	gezelter	1047
222			W_l_hat = W_l / pow(QSq_l, 1.5);
223
224			writeOrderParameter(Q_l, real(W_l_hat));
225			}
226	chuckv	1038
227
228	gezelter	1047	void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
229	chuckv	1038
230	gezelter	1047	std::ofstream os(getOutputFileName().c_str());
231
232			if (os.is_open()) {
233	gezelter	1041
234	gezelter	1047	os << "# Bond Order Parameters\n";
235			os << "# selection: (" << selectionScript_ << ")\n";
236			os << "# \n";
237			os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
238			os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
239			os.close();
240
241	gezelter	1041	} else {
242			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
243	gezelter	1047	getOutputFileName().c_str());
244	gezelter	1041	painCave.isFatal = 1;
245			simError();
246			}
247			}
248	gezelter	1039	}