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;   

    // Q can take values from 0 to 1

    MinQ_ = 0.0;
    MaxQ_ = 3.0;
    deltaQ_ = (MaxQ_ - MinQ_) / nbins;
    Q_histogram_.resize(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_ = -0.18;
    MaxW_ = 0.18;
    deltaW_ = (MaxW_ - MinW_) / nbins;
    W_histogram_.resize(nbins);

  }

  BondOrderParameter::~BondOrderParameter() {
    Q_histogram_.clear();
    W_histogram_.clear();
  }

  void BondOrderParameter::initalizeHistogram() {
    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
    std::fill(W_histogram_.begin(), W_histogram_.end(), 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;
    RealType dist;
    std::map<int,ComplexType> q_lm;
    std::map<int,ComplexType> QBar_lm;
    RealType QSq_l;
    RealType Q_l;
    ComplexType W_l;
    ComplexType W_l_hat;
    int nBonds, 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();
        }        
      }           
            
      // 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 m = -lNumber_; m <= lNumber_; m++) {
          q_lm[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();       
              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);
                  q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
                }
                nBonds++;
              }  
            }
          }
        }
        RealType ql = 0.0;
        for(int m=-lNumber_; m<=lNumber_; m++) {          
          ql += norm(QBar_lm[m]);
        }        
        ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
        collectHistogram(sqrt(ql)/(RealType)nBonds);

        Nbonds += nBonds;
        for (int m=-lNumber_; m<=lNumber_; m++) {
          QBar_lm[m] += q_lm[m];
        }
      }
    }

    // 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::collectHistogram(RealType q_l) {

    if (q_l >= MinQ_ && q_l < MaxQ_) {
      int qbin = (q_l - MinQ_) / deltaQ_;
      Q_histogram_[qbin] += 1;
      Qcount_++;
      sumQ_ += q_l;
      sumQ2_ += q_l * q_l;
    } else {
      sprintf( painCave.errMsg,
               "q_l value outside reasonable range\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();  
    }

  }  


  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";
      // Normalize by number of frames and write it out:
      for (int i = 0; i < Q_histogram_.size(); ++i) {
        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
        osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
      }

      os.close();

    } else {
      sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", 
              getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();  
    }
  }
}
Revision:	3017
Committed:	Fri Sep 22 01:36:27 2006 UTC (17 years, 10 months ago) by gezelter
File size:	9933 byte(s)
Log Message:	Following Rein ten Wolde article
#	User	Rev	Content
1	chuckv	3005	/*
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	3007
49	chuckv	3005	#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	3010	#include "math/SphericalHarmonic.hpp"
55	gezelter	3009
56	chuckv	3005	namespace oopse {
57
58	gezelter	3007	BondOrderParameter::BondOrderParameter(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61	gezelter	3009	double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62	gezelter	3007
63	gezelter	3009	setOutputName(getPrefix(filename) + ".bo");
64	chuckv	3005
65	gezelter	3007	evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68	chuckv	3005	}
69
70	gezelter	3007	// Set up cutoff radius and order of the Legendre Polynomial:
71
72	chuckv	3005	lNumber_ = lNumber;
73			rCut_ = rCut;
74	gezelter	3017	mSize_ = 2*lNumber_+1;
75
76			// Q can take values from 0 to 1
77
78			MinQ_ = 0.0;
79			MaxQ_ = 3.0;
80			deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81			Q_histogram_.resize(nbins);
82
83			// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
84			// use values for MinW_ and MaxW_ that are slightly larger than this:
85
86			MinW_ = -0.18;
87			MaxW_ = 0.18;
88			deltaW_ = (MaxW_ - MinW_) / nbins;
89			W_histogram_.resize(nbins);
90
91	gezelter	3007	}
92	chuckv	3005
93	gezelter	3009	BondOrderParameter::~BondOrderParameter() {
94	gezelter	3017	Q_histogram_.clear();
95			W_histogram_.clear();
96	gezelter	3009	}
97
98	gezelter	3017	void BondOrderParameter::initalizeHistogram() {
99			std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
100			std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
101			}
102
103	gezelter	3007	void BondOrderParameter::process() {
104			Molecule* mol;
105			Atom* atom;
106			RigidBody* rb;
107	gezelter	3011	int myIndex;
108	gezelter	3007	SimInfo::MoleculeIterator mi;
109			Molecule::RigidBodyIterator rbIter;
110			Molecule::AtomIterator ai;
111			StuntDouble* sd;
112	gezelter	3011	Vector3d vec;
113	gezelter	3010	RealType costheta;
114	gezelter	3007	RealType phi;
115			RealType r;
116			RealType dist;
117	gezelter	3017	std::map<int,ComplexType> q_lm;
118	gezelter	3014	std::map<int,ComplexType> QBar_lm;
119	gezelter	3007	RealType QSq_l;
120			RealType Q_l;
121	gezelter	3011	ComplexType W_l;
122			ComplexType W_l_hat;
123	gezelter	3017	int nBonds, Nbonds;
124	gezelter	3010	SphericalHarmonic sphericalHarmonic;
125	gezelter	3007	int i, j;
126	gezelter	3011	// Make arrays for Wigner3jm
127			double* THRCOF = new double[mSize_];
128			// Variables for Wigner routine
129			double l_ = (double)lNumber_;
130			double m1Pass, m2Min, m2Max;
131			int error, m1, m2, m3;
132
133	gezelter	3008	// Set the l for the spherical harmonic, it doesn't change
134			sphericalHarmonic.setL(lNumber_);
135
136	gezelter	3007	DumpReader reader(info_, dumpFilename_);
137			int nFrames = reader.getNFrames();
138	gezelter	3009	frameCounter_ = 0;
139	chuckv	3005
140	gezelter	3007	for (int istep = 0; istep < nFrames; istep += step_) {
141			reader.readFrame(istep);
142	gezelter	3009	frameCounter_++;
143	gezelter	3007	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
144
145			if (evaluator_.isDynamic()) {
146			seleMan_.setSelectionSet(evaluator_.evaluate());
147			}
148	chuckv	3005
149	gezelter	3007	// update the positions of atoms which belong to the rigidbodies
150	chuckv	3005
151	gezelter	3007	for (mol = info_->beginMolecule(mi); mol != NULL;
152			mol = info_->nextMolecule(mi)) {
153			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
154			rb = mol->nextRigidBody(rbIter)) {
155			rb->updateAtoms();
156			}
157	gezelter	3017	}
158
159	gezelter	3007	// outer loop is over the selected StuntDoubles:
160	chuckv	3005
161	gezelter	3007	for (sd = seleMan_.beginSelected(i); sd != NULL;
162			sd = seleMan_.nextSelected(i)) {
163	chuckv	3005
164	gezelter	3011	myIndex = sd->getGlobalIndex();
165	gezelter	3017	nBonds = 0;
166			for (int m = -lNumber_; m <= lNumber_; m++) {
167			q_lm[m] = 0.0;
168			}
169	gezelter	3007
170			// inner loop is over all other atoms in the system:
171
172			for (mol = info_->beginMolecule(mi); mol != NULL;
173			mol = info_->nextMolecule(mi)) {
174			for (atom = mol->beginAtom(ai); atom != NULL;
175			atom = mol->nextAtom(ai)) {
176	chuckv	3005
177	gezelter	3011	if (atom->getGlobalIndex() != myIndex) {
178	chuckv	3005
179	gezelter	3011	vec = sd->getPos() - atom->getPos();
180			currentSnapshot_->wrapVector(vec);
181	gezelter	3010
182	gezelter	3011	// Calculate "bonds" and build Q_lm(r) where
183			// Q_lm = Y_lm(theta(r),phi(r))
184			// The spherical harmonics are wrt any arbitrary coordinate
185			// system, we choose standard spherical coordinates
186
187			r = vec.length();
188
189			// Check to see if neighbor is in bond cutoff
190
191			if (r < rCut_) {
192			costheta = vec.z() / r;
193			phi = atan2(vec.y(), vec.x());
194
195			for(int m = -lNumber_; m <= lNumber_; m++){
196			sphericalHarmonic.setM(m);
197	gezelter	3017	q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
198	gezelter	3011	}
199			nBonds++;
200			}
201			}
202	gezelter	3007	}
203			}
204	gezelter	3017	RealType ql = 0.0;
205			for(int m=-lNumber_; m<=lNumber_; m++) {
206			ql += norm(QBar_lm[m]);
207			}
208			ql = 4.0NumericConstant::PI/(RealType)(2*lNumber_+1);
209			collectHistogram(sqrt(ql)/(RealType)nBonds);
210
211			Nbonds += nBonds;
212			for (int m=-lNumber_; m<=lNumber_; m++) {
213			QBar_lm[m] += q_lm[m];
214			}
215			}
216	gezelter	3015	}
217	chuckv	3005
218	gezelter	3015	// Normalize Qbar2
219			for (int m = -lNumber_;m <= lNumber_; m++){
220	gezelter	3017	QBar_lm[m] /= Nbonds;
221	gezelter	3007	}
222
223	gezelter	3015	// Find second order invariant Q_l
224	gezelter	3007
225	gezelter	3015	QSq_l = 0.0;
226			for (int m = -lNumber_; m <= lNumber_; m++){
227			QSq_l += norm(QBar_lm[m]);
228	gezelter	3007	}
229	gezelter	3015
230			std::cout << "qsl = " << QSq_l << "\n";
231			Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
232
233			// Find Third Order Invariant W_l
234
235			W_l = 0.0;
236			for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
237			// Zero work array
238			for (int ii = 0; ii < mSize_; ii++){
239			THRCOF[ii] = 0.0;
240			}
241			// Get Wigner coefficients
242			m1Pass = (double)m1;
243	gezelter	3009
244	gezelter	3015	Wigner3jm(&l_, &l_, &l_,
245			&m1Pass, &m2Min, &m2Max,
246			THRCOF, &mSize_, &error);
247	gezelter	3009
248	gezelter	3015	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
249			m2 = (int)floor(m2Min) + mmm;
250			m3 = -m1-m2;
251			W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
252	gezelter	3009	}
253	gezelter	3007	}
254	gezelter	3015
255			W_l_hat = W_l / pow(QSq_l, 1.5);
256
257			writeOrderParameter(Q_l, real(W_l_hat));
258			}
259	chuckv	3005
260	gezelter	3017	void BondOrderParameter::collectHistogram(RealType q_l) {
261	chuckv	3005
262	gezelter	3017	if (q_l >= MinQ_ && q_l < MaxQ_) {
263			int qbin = (q_l - MinQ_) / deltaQ_;
264			Q_histogram_[qbin] += 1;
265			Qcount_++;
266			sumQ_ += q_l;
267			sumQ2_ += q_l * q_l;
268			} else {
269			sprintf( painCave.errMsg,
270			"q_l value outside reasonable range\n");
271			painCave.severity = OOPSE_ERROR;
272			painCave.isFatal = 1;
273			simError();
274			}
275
276			}
277
278
279	gezelter	3015	void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
280	chuckv	3005
281	gezelter	3015	std::ofstream os(getOutputFileName().c_str());
282
283			if (os.is_open()) {
284	gezelter	3009
285	gezelter	3015	os << "# Bond Order Parameters\n";
286			os << "# selection: (" << selectionScript_ << ")\n";
287			os << "# \n";
288			os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
289			os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
290	gezelter	3017	// Normalize by number of frames and write it out:
291			for (int i = 0; i < Q_histogram_.size(); ++i) {
292			RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
293			osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n";
294			}
295
296	gezelter	3015	os.close();
297
298	gezelter	3009	} else {
299			sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
300	gezelter	3015	getOutputFileName().c_str());
301	gezelter	3009	painCave.isFatal = 1;
302			simError();
303			}
304			}
305	gezelter	3007	}