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/RealSphericalHarmonic.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) + ".obo");

    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;    

    deltaQ_ = 1.0 / nbins;
    deltaW_ = 2.0 / nbins;

    Q_histogram_.resize(nbins);
    W_histogram_.resize(nbins);

  }

  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;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator ai;
    StuntDouble* sd;
    RealType theta;
    RealType phi;
    RealType r;
    RealType dist;
    std::map<int, RealType> QBar_lm;
    RealType QSq_l;
    RealType Q_l;
    int nBonds;
    RealSphericalHarmonic sphericalHarmonic;
    int i, j;
  
    // Set the l for the spherical harmonic, it doesn't change
    sphericalHarmonic.setL(lNumber_);


    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();


    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      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)) {

        // For this central atom, zero out nBonds and QBar_lm

        nBonds = 0;
       
        for (int m = -lNumber_; m <= lNumber_; m++) {
          QBar_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)) {


            Vector3d 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 = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
            
            // Check to see if neighbor is in bond cutoff 
            
            if (r < rCut_) {            
              theta = atan2(vec.y(), vec.x());
              phi = acos(vec.z()/r);
              for(int m = -lNumber_; m <= lNumber_; m++){
                sphericalHarmonic.setM(m);
                QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
              }
              nBonds++;
            }  
          }
        }
        
        // Normalize Qbar
        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 += pow(QBar_lm[m], 2);  
        }
        Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
     
        // Find Third Order Invariant W_l

        // Make arrays for Wigner3jm
        double* THRCOF = new double[mSize_];
        // Variables for Wigner routine
        double l_ = (double)lNumber_;
        double m2Min, m2Max;
        int error, m1, m2, m3;

        RealType W_l;
        RealType W_l_hat;
        W_l = 0.0;
        for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
          // Zero work array
          for (int ii = 0; ii < mSize_; ii++){
            THRCOF[i] = 0.0;
          }
          // Get Wigner coefficients
          Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
          for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
            m2 = floor(m2Min) + m_index - 1;
            m3 = -m1-m2;
            W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
          }
        }

        W_l_hat = W_l / pow(QSq_l, 1.5);

        // accumulate histogram data for Q_l and W_l_hat:

        collectHistogram(Q_l, W_l_hat);
                
      }
    }
    
    // Normalize by number of frames
    for (int m = -lNumber_; m <= lNumber_; m++){
      QBar_lm[m] /=  nFrames;   
    }
    
     
    writeOrderParameter();
    
  }

  
  void BondOrderParameter::processHistogram() {
    
    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume * 2.0;
    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

    for(int i = 0 ; i < histogram_.size(); ++i){

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
      RealType nIdeal = volSlice * pairConstant;

      avgGofr_[i] += histogram_[i] / nIdeal;    
    }

  }

  void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {

    if (Q_l < MaxQ_) {
      int whichBin = Q_l / deltaQ_;
      Q_histogram_[whichBin] += 1;
    }
    if (W_l_hat < MaxW_) {
      int whichBin = W_l_hat / deltaW_;
      W_histogram_[whichBin] += 1;
    }
  }
  

  void BondOrderParameter::writeOrderParameter() {

    std::ofstream os(getOutputFileName().c_str());
    os << "#Bond Order Parameter\n";
    os << "#selection: (" << selectionScript_ << ")\n";

    for (std::size_t i = 0; i < orderParams_.size(); ++i) {
      os <<  orderParams_[i].p2 << "\t"
         <<  orderParams_[i].director[0] << "\t"
         <<  orderParams_[i].director[1] << "\t"
         <<  orderParams_[i].director[2] << "\t"
         <<  orderParams_[i].angle << "\n";

    }
  }


}
Revision:	3008
Committed:	Tue Sep 19 21:20:15 2006 UTC (17 years, 10 months ago) by gezelter
File size:	9407 byte(s)
Log Message:	Adding BondOrderParameter to StaticProps
#	Content
1	/*
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
49	#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	#include "math/RealSphericalHarmonic.hpp"
55	namespace oopse {
56
57
58	BondOrderParameter::BondOrderParameter(SimInfo* info,
59	const std::string& filename,
60	const std::string& sele,
61	double rCut, int lNumber, int nbins)
62	: StaticAnalyser(info, filename), selectionScript_(sele),
63	evaluator_(info), seleMan_(info){
64
65	setOutputName(getPrefix(filename) + ".obo");
66
67	evaluator_.loadScriptString(sele);
68	if (!evaluator_.isDynamic()) {
69	seleMan_.setSelectionSet(evaluator_.evaluate());
70	}
71
72	// Set up cutoff radius and order of the Legendre Polynomial:
73
74	lNumber_ = lNumber;
75	rCut_ = rCut;
76	mSize_ = 2*lNumber_+1;
77
78	deltaQ_ = 1.0 / nbins;
79	deltaW_ = 2.0 / nbins;
80
81	Q_histogram_.resize(nbins);
82	W_histogram_.resize(nbins);
83
84	}
85
86	void BondOrderParameter::initalizeHistogram() {
87	std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
88	std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
89	}
90
91	void BondOrderParameter::process() {
92	Molecule* mol;
93	Atom* atom;
94	RigidBody* rb;
95	SimInfo::MoleculeIterator mi;
96	Molecule::RigidBodyIterator rbIter;
97	Molecule::AtomIterator ai;
98	StuntDouble* sd;
99	RealType theta;
100	RealType phi;
101	RealType r;
102	RealType dist;
103	std::map<int, RealType> QBar_lm;
104	RealType QSq_l;
105	RealType Q_l;
106	int nBonds;
107	RealSphericalHarmonic sphericalHarmonic;
108	int i, j;
109
110	// Set the l for the spherical harmonic, it doesn't change
111	sphericalHarmonic.setL(lNumber_);
112
113
114	DumpReader reader(info_, dumpFilename_);
115	int nFrames = reader.getNFrames();
116
117
118	for (int istep = 0; istep < nFrames; istep += step_) {
119	reader.readFrame(istep);
120	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
121
122	if (evaluator_.isDynamic()) {
123	seleMan_.setSelectionSet(evaluator_.evaluate());
124	}
125
126	// update the positions of atoms which belong to the rigidbodies
127
128	for (mol = info_->beginMolecule(mi); mol != NULL;
129	mol = info_->nextMolecule(mi)) {
130	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
131	rb = mol->nextRigidBody(rbIter)) {
132	rb->updateAtoms();
133	}
134	}
135
136	// outer loop is over the selected StuntDoubles:
137
138	for (sd = seleMan_.beginSelected(i); sd != NULL;
139	sd = seleMan_.nextSelected(i)) {
140
141	// For this central atom, zero out nBonds and QBar_lm
142
143	nBonds = 0;
144
145	for (int m = -lNumber_; m <= lNumber_; m++) {
146	QBar_lm[m] = 0.0;
147	}
148
149	// inner loop is over all other atoms in the system:
150
151	for (mol = info_->beginMolecule(mi); mol != NULL;
152	mol = info_->nextMolecule(mi)) {
153	for (atom = mol->beginAtom(ai); atom != NULL;
154	atom = mol->nextAtom(ai)) {
155
156
157	Vector3d vec = sd->getPos() - atom->getPos();
158	currentSnapshot_->wrapVector(vec);
159
160	// 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 = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
166
167	// Check to see if neighbor is in bond cutoff
168
169	if (r < rCut_) {
170	theta = atan2(vec.y(), vec.x());
171	phi = acos(vec.z()/r);
172	for(int m = -lNumber_; m <= lNumber_; m++){
173	sphericalHarmonic.setM(m);
174	QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
175	}
176	nBonds++;
177	}
178	}
179	}
180
181	// Normalize Qbar
182	for (int m = -lNumber_;m <= lNumber_; m++){
183	QBar_lm[m] /= nBonds;
184	}
185
186	// Find second order invariant Q_l
187
188	QSq_l = 0.0;
189	for (int m = -lNumber_; m <= lNumber_; m++){
190	QSq_l += pow(QBar_lm[m], 2);
191	}
192	Q_l = sqrt(QSq_l(4.0 NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
193
194	// Find Third Order Invariant W_l
195
196	// Make arrays for Wigner3jm
197	double* THRCOF = new double[mSize_];
198	// Variables for Wigner routine
199	double l_ = (double)lNumber_;
200	double m2Min, m2Max;
201	int error, m1, m2, m3;
202
203	RealType W_l;
204	RealType W_l_hat;
205	W_l = 0.0;
206	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
207	// Zero work array
208	for (int ii = 0; ii < mSize_; ii++){
209	THRCOF[i] = 0.0;
210	}
211	// Get Wigner coefficients
212	Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
213	for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
214	m2 = floor(m2Min) + m_index - 1;
215	m3 = -m1-m2;
216	W_l += THRCOF[m_index]QBar_lm[m1+lNumber_]QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
217	}
218	}
219
220	W_l_hat = W_l / pow(QSq_l, 1.5);
221
222	// accumulate histogram data for Q_l and W_l_hat:
223
224	collectHistogram(Q_l, W_l_hat);
225
226	}
227	}
228
229	// Normalize by number of frames
230	for (int m = -lNumber_; m <= lNumber_; m++){
231	QBar_lm[m] /= nFrames;
232	}
233
234
235
236
237
238	writeOrderParameter();
239
240	}
241
242
243	void BondOrderParameter::processHistogram() {
244
245	int nPairs = getNPairs();
246	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
247	RealType pairDensity = nPairs /volume * 2.0;
248	RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
249
250	for(int i = 0 ; i < histogram_.size(); ++i){
251
252	RealType rLower = i * deltaR_;
253	RealType rUpper = rLower + deltaR_;
254	RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
255	RealType nIdeal = volSlice * pairConstant;
256
257	avgGofr_[i] += histogram_[i] / nIdeal;
258	}
259
260	}
261
262	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
263
264	if (Q_l < MaxQ_) {
265	int whichBin = Q_l / deltaQ_;
266	Q_histogram_[whichBin] += 1;
267	}
268	if (W_l_hat < MaxW_) {
269	int whichBin = W_l_hat / deltaW_;
270	W_histogram_[whichBin] += 1;
271	}
272	}
273
274
275	void BondOrderParameter::writeOrderParameter() {
276
277	std::ofstream os(getOutputFileName().c_str());
278	os << "#Bond Order Parameter\n";
279	os << "#selection: (" << selectionScript_ << ")\n";
280
281	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
282	os << orderParams_[i].p2 << "\t"
283	<< orderParams_[i].director[0] << "\t"
284	<< orderParams_[i].director[1] << "\t"
285	<< orderParams_[i].director[2] << "\t"
286	<< orderParams_[i].angle << "\n";
287
288	}
289	}
290
291
292
293	}