ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-4/src/applications/staticProps/BondOrderParameter.cpp
Revision: 3010
Committed: Wed Sep 20 22:16:23 2006 UTC (17 years, 10 months ago) by gezelter
File size: 11044 byte(s)
Log Message:
added SphericalHarmonics, fixed a few problems with BondOrderParameter

File Contents

# 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/SphericalHarmonic.hpp"
55
56 namespace oopse {
57
58 BondOrderParameter::BondOrderParameter(SimInfo* info,
59 const std::string& filename,
60 const std::string& sele,
61 double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
62
63 setOutputName(getPrefix(filename) + ".bo");
64
65 evaluator_.loadScriptString(sele);
66 if (!evaluator_.isDynamic()) {
67 seleMan_.setSelectionSet(evaluator_.evaluate());
68 }
69
70 // Set up cutoff radius and order of the Legendre Polynomial:
71
72 lNumber_ = lNumber;
73 rCut_ = rCut;
74 mSize_ = 2*lNumber_+1;
75
76 // Q can take values from 0 to 1
77
78 MinQ_ = 0.0;
79 MaxQ_ = 1.0;
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 }
92
93 BondOrderParameter::~BondOrderParameter() {
94 Q_histogram_.clear();
95 W_histogram_.clear();
96 }
97
98 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 void BondOrderParameter::process() {
104 Molecule* mol;
105 Atom* atom;
106 RigidBody* rb;
107 SimInfo::MoleculeIterator mi;
108 Molecule::RigidBodyIterator rbIter;
109 Molecule::AtomIterator ai;
110 StuntDouble* sd;
111 RealType costheta;
112 RealType phi;
113 RealType r;
114 RealType dist;
115 std::map<int, ComplexType> QBar_lm;
116 RealType QSq_l;
117 RealType Q_l;
118 int nBonds;
119 SphericalHarmonic sphericalHarmonic;
120 int i, j;
121
122 // Set the l for the spherical harmonic, it doesn't change
123 sphericalHarmonic.setL(lNumber_);
124
125
126 DumpReader reader(info_, dumpFilename_);
127 int nFrames = reader.getNFrames();
128 frameCounter_ = 0;
129
130 for (int istep = 0; istep < nFrames; istep += step_) {
131 reader.readFrame(istep);
132 frameCounter_++;
133 currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
134
135 if (evaluator_.isDynamic()) {
136 seleMan_.setSelectionSet(evaluator_.evaluate());
137 }
138
139 // update the positions of atoms which belong to the rigidbodies
140
141 for (mol = info_->beginMolecule(mi); mol != NULL;
142 mol = info_->nextMolecule(mi)) {
143 for (rb = mol->beginRigidBody(rbIter); rb != NULL;
144 rb = mol->nextRigidBody(rbIter)) {
145 rb->updateAtoms();
146 }
147 }
148
149 // outer loop is over the selected StuntDoubles:
150
151 for (sd = seleMan_.beginSelected(i); sd != NULL;
152 sd = seleMan_.nextSelected(i)) {
153
154 // For this central atom, zero out nBonds and QBar_lm
155
156 nBonds = 0;
157
158 for (int m = -lNumber_; m <= lNumber_; m++) {
159 QBar_lm[m] = 0.0;
160 }
161
162 // inner loop is over all other atoms in the system:
163
164 for (mol = info_->beginMolecule(mi); mol != NULL;
165 mol = info_->nextMolecule(mi)) {
166 for (atom = mol->beginAtom(ai); atom != NULL;
167 atom = mol->nextAtom(ai)) {
168
169
170 Vector3d vec = sd->getPos() - atom->getPos();
171 currentSnapshot_->wrapVector(vec);
172
173 // Calculate "bonds" and build Q_lm(r) where
174 // Q_lm = Y_lm(theta(r),phi(r))
175 // The spherical harmonics are wrt any arbitrary coordinate
176 // system, we choose standard spherical coordinates
177
178 r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
179
180 // Check to see if neighbor is in bond cutoff
181
182 if (r < rCut_) {
183 costheta = vec.z() / r;
184 phi = atan2(vec.y(), vec.x());
185
186 for(int m = -lNumber_; m <= lNumber_; m++){
187 sphericalHarmonic.setM(m);
188 QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
189 }
190 nBonds++;
191 }
192 }
193 }
194
195 // Normalize Qbar2
196 for (int m = -lNumber_;m <= lNumber_; m++){
197 QBar_lm[m] /= nBonds;
198 }
199
200 // Find second order invariant Q_l
201
202 QSq_l = 0.0;
203 for (int m = -lNumber_; m <= lNumber_; m++){
204 QSq_l += norm(QBar_lm[m]);
205 }
206 Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
207
208 // Find Third Order Invariant W_l
209
210 // Make arrays for Wigner3jm
211 double* THRCOF = new double[mSize_];
212 // Variables for Wigner routine
213 double l_ = (double)lNumber_;
214 double m1Pass, m2Min, m2Max;
215 int error, m1, m2, m3;
216
217 ComplexType W_l;
218 ComplexType W_l_hat;
219 W_l = 0.0;
220 for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
221 // Zero work array
222 for (int ii = 0; ii < mSize_; ii++){
223 THRCOF[i] = 0.0;
224 }
225 // Get Wigner coefficients
226 m1Pass = (double)m1;
227 Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
228 for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
229 m2 = floor(m2Min) + m_index - 1;
230 m3 = -m1-m2;
231 W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
232 }
233 }
234
235 W_l_hat = W_l / pow(QSq_l, 1.5);
236
237 // accumulate histogram data for Q_l and W_l_hat:
238
239 collectHistogram(Q_l, real(W_l_hat));
240
241 }
242 }
243
244 writeOrderParameter();
245
246 }
247
248
249 void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
250
251 if (Q_l >= MinQ_ && Q_l < MaxQ_) {
252 int qbin = (Q_l - MinQ_) / deltaQ_;
253 Q_histogram_[qbin] += 1;
254 Qcount_++;
255 sumQ_ += Q_l;
256 sumQ2_ += Q_l * Q_l;
257 } else {
258 sprintf( painCave.errMsg,
259 "Q_l value outside reasonable range\n");
260 painCave.severity = OOPSE_ERROR;
261 painCave.isFatal = 1;
262 simError();
263 }
264
265 if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
266 int wbin = (W_l_hat - MinW_) / deltaW_;
267 W_histogram_[wbin] += 1;
268 Wcount_++;
269 sumW_ += W_l_hat;
270 sumW2_ += W_l_hat*W_l_hat;
271 } else {
272 sprintf( painCave.errMsg,
273 "W_l_hat value outside reasonable range\n");
274 painCave.severity = OOPSE_ERROR;
275 painCave.isFatal = 1;
276 simError();
277 }
278 }
279
280 void BondOrderParameter::writeOrderParameter() {
281
282 std::ofstream osq((getOutputFileName() + "q").c_str());
283
284 if (osq.is_open()) {
285
286 RealType qAvg = sumQ_ / (RealType) Qcount_;
287 RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
288
289 osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
290 osq << "# selection: (" << selectionScript_ << ")\n";
291 osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
292 osq << "# std. dev.: " << qStdDev << "\n";
293
294 // Normalize by number of frames and write it out:
295 for (int i = 0; i < Q_histogram_.size(); ++i) {
296 RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
297 osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
298 }
299
300 osq.close();
301 } else {
302 sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
303 (getOutputFileName() + "q").c_str());
304 painCave.isFatal = 1;
305 simError();
306 }
307
308 std::ofstream osw((getOutputFileName() + "w").c_str());
309
310 if (osw.is_open()) {
311
312 RealType wAvg = sumW_ / (RealType) Wcount_;
313 RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
314
315 osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
316 osw << "# selection: (" << selectionScript_ << ")\n";
317 osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
318 osw << "# std. dev.: " << wStdDev << "\n";
319
320 // Normalize by number of frames and write it out:
321 for (int i = 0; i < W_histogram_.size(); ++i) {
322 RealType Wval = MinW_ + (i + 0.5) * deltaW_;
323 osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
324 }
325
326 osw.close();
327 } else {
328 sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
329 (getOutputFileName() + "w").c_str());
330 painCave.isFatal = 1;
331 simError();
332 }
333 }
334 }

Properties

Name Value
svn:executable *