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root/OpenMD/branches/development/src/applications/staticProps/BondOrderParameter.cpp

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trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents), Revision 1040 by gezelter, Tue Sep 19 21:20:15 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
32	+	* 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	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	+	*  Created by J. Daniel Gezelter on 09/26/06.
42	+	*  @author  J. Daniel Gezelter
43	+	*  @version $Id$
44	+	*
45		*/
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	–	*/
46
47		#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	<	#include "math/RealSphericalHarmonic.hpp"
55	<	namespace oopse {
52	>	#include "math/Wigner3jm.hpp"
53
54	+	using namespace MATPACK;
55	+	namespace OpenMD {
56
57		BondOrderParameter::BondOrderParameter(SimInfo* info,
58		const std::string& filename,
59		const std::string& sele,
60	<	double rCut, int lNumber, int nbins)
62	<	: StaticAnalyser(info, filename), selectionScript_(sele),
63	<	evaluator_(info), seleMan_(info){
60	>	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61
62	<	setOutputName(getPrefix(filename) + ".obo");
62	>	setOutputName(getPrefix(filename) + ".bo");
63
64		evaluator_.loadScriptString(sele);
65		if (!evaluator_.isDynamic()) {
#	Line 71 | Line 68 | namespace oopse {
68
69		// Set up cutoff radius and order of the Legendre Polynomial:
70
74	–	lNumber_ = lNumber;
71		rCut_ = rCut;
72	<	mSize_ = 2*lNumber_+1;
72	>	nBins_ = nbins;
73	>	Qcount_.resize(lMax_+1);
74	>	Wcount_.resize(lMax_+1);
75
76	<	deltaQ_ = 1.0 / nbins;
79	<	deltaW_ = 2.0 / nbins;
76	>	// Q can take values from 0 to 1
77
78	<	Q_histogram_.resize(nbins);
79	<	W_histogram_.resize(nbins);
78	>	MinQ_ = 0.0;
79	>	MaxQ_ = 1.1;
80	>	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81
82	<	}
82	>	// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
83	>	// use values for MinW_ and MaxW_ that are slightly larger than this:
84
85	+	MinW_ = -1.1;
86	+	MaxW_ = 1.1;
87	+	deltaW_ = (MaxW_ - MinW_) / nbins;
88	+
89	+	// Make arrays for Wigner3jm
90	+	RealType* THRCOF = new RealType[2*lMax_+1];
91	+	// Variables for Wigner routine
92	+	RealType lPass, m1Pass, m2m, m2M;
93	+	int error, mSize;
94	+	mSize = 2*lMax_+1;
95	+
96	+	for (int l = 0; l <= lMax_; l++) {
97	+	lPass = (RealType)l;
98	+	for (int m1 = -l; m1 <= l; m1++) {
99	+	m1Pass = (RealType)m1;
100	+
101	+	std::pair<int,int> lm = std::make_pair(l, m1);
102	+
103	+	// Zero work array
104	+	for (int ii = 0; ii < 2*l + 1; ii++){
105	+	THRCOF[ii] = 0.0;
106	+	}
107	+
108	+	// Get Wigner coefficients
109	+	Wigner3jm(lPass, lPass, lPass,
110	+	m1Pass, m2m, m2M,
111	+	THRCOF, mSize, error);
112	+
113	+	m2Min[lm] = (int)floor(m2m);
114	+	m2Max[lm] = (int)floor(m2M);
115	+
116	+	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
117	+	w3j[lm].push_back(THRCOF[mmm]);
118	+	}
119	+	}
120	+	}
121	+	delete [] THRCOF;
122	+	THRCOF = NULL;
123	+	}
124	+
125	+	BondOrderParameter::~BondOrderParameter() {
126	+	Q_histogram_.clear();
127	+	W_histogram_.clear();
128	+	for (int l = 0; l <= lMax_; l++) {
129	+	for (int m = -l; m <= l; m++) {
130	+	w3j[std::make_pair(l,m)].clear();
131	+	}
132	+	}
133	+	w3j.clear();
134	+	m2Min.clear();
135	+	m2Max.clear();
136	+	}
137	+
138		void BondOrderParameter::initalizeHistogram() {
139	<	std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
140	<	std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
139	>	for (int bin = 0; bin < nBins_; bin++) {
140	>	for (int l = 0; l <= lMax_; l++) {
141	>	Q_histogram_[std::make_pair(bin,l)] = 0;
142	>	W_histogram_[std::make_pair(bin,l)] = 0;
143	>	}
144	>	}
145		}
146
147		void BondOrderParameter::process() {
148		Molecule* mol;
149		Atom* atom;
150		RigidBody* rb;
151	+	int myIndex;
152		SimInfo::MoleculeIterator mi;
153		Molecule::RigidBodyIterator rbIter;
154		Molecule::AtomIterator ai;
155		StuntDouble* sd;
156	<	RealType theta;
156	>	Vector3d vec;
157	>	RealType costheta;
158		RealType phi;
159		RealType r;
160	<	RealType dist;
161	<	std::map<int, RealType> QBar_lm;
162	<	RealType QSq_l;
163	<	RealType Q_l;
164	<	int nBonds;
165	<	RealSphericalHarmonic sphericalHarmonic;
166	<	int i, j;
167	<
168	<	// Set the l for the spherical harmonic, it doesn't change
169	<	sphericalHarmonic.setL(lNumber_);
160	>	std::map<std::pair<int,int>,ComplexType> q;
161	>	std::vector<RealType> q_l;
162	>	std::vector<RealType> q2;
163	>	std::vector<ComplexType> w;
164	>	std::vector<ComplexType> w_hat;
165	>	std::map<std::pair<int,int>,ComplexType> QBar;
166	>	std::vector<RealType> Q2;
167	>	std::vector<RealType> Q;
168	>	std::vector<ComplexType> W;
169	>	std::vector<ComplexType> W_hat;
170	>	int nBonds, Nbonds;
171	>	SphericalHarmonic sphericalHarmonic;
172	>	int i;
173
113	–
174		DumpReader reader(info_, dumpFilename_);
175		int nFrames = reader.getNFrames();
176	+	frameCounter_ = 0;
177
178	+	q_l.resize(lMax_+1);
179	+	q2.resize(lMax_+1);
180	+	w.resize(lMax_+1);
181	+	w_hat.resize(lMax_+1);
182
183	+	Q2.resize(lMax_+1);
184	+	Q.resize(lMax_+1);
185	+	W.resize(lMax_+1);
186	+	W_hat.resize(lMax_+1);
187	+	Nbonds = 0;
188	+
189		for (int istep = 0; istep < nFrames; istep += step_) {
190		reader.readFrame(istep);
191	+	frameCounter_++;
192		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
193
194		if (evaluator_.isDynamic()) {
#	Line 131 | Line 203 | namespace oopse {
203		rb = mol->nextRigidBody(rbIter)) {
204		rb->updateAtoms();
205		}
206	<	}
207	<
206	>	}
207	>
208		// outer loop is over the selected StuntDoubles:
209
210		for (sd = seleMan_.beginSelected(i); sd != NULL;
211		sd = seleMan_.nextSelected(i)) {
212
213	<	// For this central atom, zero out nBonds and QBar_lm
142	<
213	>	myIndex = sd->getGlobalIndex();
214		nBonds = 0;
215	<
216	<	for (int m = -lNumber_; m <= lNumber_; m++) {
217	<	QBar_lm[m] = 0.0;
215	>
216	>	for (int l = 0; l <= lMax_; l++) {
217	>	for (int m = -l; m <= l; m++) {
218	>	q[std::make_pair(l,m)] = 0.0;
219	>	}
220		}
221
222		// inner loop is over all other atoms in the system:
#	Line 153 | Line 226 | namespace oopse {
226		for (atom = mol->beginAtom(ai); atom != NULL;
227		atom = mol->nextAtom(ai)) {
228
229	+	if (atom->getGlobalIndex() != myIndex) {
230
231	<	Vector3d vec = sd->getPos() - atom->getPos();
232	<	currentSnapshot_->wrapVector(vec);
233	<
234	<	// Calculate "bonds" and build Q_lm(r) where
235	<	//      Q_lm = Y_lm(theta(r),phi(r))
236	<	// The spherical harmonics are wrt any arbitrary coordinate
237	<	// system, we choose standard spherical coordinates
238	<
239	<	r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
240	<
241	<	// Check to see if neighbor is in bond cutoff
242	<
243	<	if (r < rCut_) {
244	<	theta = atan2(vec.y(), vec.x());
245	<	phi = acos(vec.z()/r);
246	<	for(int m = -lNumber_; m <= lNumber_; m++){
247	<	sphericalHarmonic.setM(m);
248	<	QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
249	<	}
250	<	nBonds++;
251	<	}
231	>	vec = sd->getPos() - atom->getPos();
232	>
233	>	if (usePeriodicBoundaryConditions_)
234	>	currentSnapshot_->wrapVector(vec);
235	>
236	>	// Calculate "bonds" and build Q_lm(r) where
237	>	//      Q_lm = Y_lm(theta(r),phi(r))
238	>	// The spherical harmonics are wrt any arbitrary coordinate
239	>	// system, we choose standard spherical coordinates
240	>
241	>	r = vec.length();
242	>
243	>	// Check to see if neighbor is in bond cutoff
244	>
245	>	if (r < rCut_) {
246	>	costheta = vec.z() / r;
247	>	phi = atan2(vec.y(), vec.x());
248	>
249	>	for (int l = 0; l <= lMax_; l++) {
250	>	sphericalHarmonic.setL(l);
251	>	for(int m = -l; m <= l; m++){
252	>	sphericalHarmonic.setM(m);
253	>	q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
254	>	}
255	>	}
256	>	nBonds++;
257	>	}
258	>	}
259		}
260		}
261
262	<	// Normalize Qbar
263	<	for (int m = -lNumber_;m <= lNumber_; m++){
264	<	QBar_lm[m] /= nBonds;
262	>
263	>	for (int l = 0; l <= lMax_; l++) {
264	>	q2[l] = 0.0;
265	>	for (int m = -l; m <= l; m++){
266	>	q[std::make_pair(l,m)] /= (RealType)nBonds;
267	>	q2[l] += norm(q[std::make_pair(l,m)]);
268	>	}
269	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
270		}
271	<
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	<
271	>
272		// Find Third Order Invariant W_l
273	<
274	<	// Make arrays for Wigner3jm
275	<	double* THRCOF = new double[mSize_];
276	<	// Variables for Wigner routine
277	<	double l_ = (double)lNumber_;
278	<	double m2Min, m2Max;
279	<	int error, m1, m2, m3;
280	<
281	<	RealType W_l;
282	<	RealType W_l_hat;
283	<	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;
273	>
274	>	for (int l = 0; l <= lMax_; l++) {
275	>	w[l] = 0.0;
276	>	for (int m1 = -l; m1 <= l; m1++) {
277	>	std::pair<int,int> lm = std::make_pair(l, m1);
278	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
279	>	int m2 = m2Min[lm] + mmm;
280	>	int m3 = -m1-m2;
281	>	w[l] += w3j[lm][mmm] * q[lm] *
282	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
283	>	}
284		}
285	<	// Get Wigner coefficients
286	<	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	<	}
285	>
286	>	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
287		}
288
289	<	W_l_hat = W_l / pow(QSq_l, 1.5);
290	<
291	<	// accumulate histogram data for Q_l and W_l_hat:
292	<
293	<	collectHistogram(Q_l, W_l_hat);
294	<
289	>	collectHistogram(q_l, w_hat);
290	>
291	>	Nbonds += nBonds;
292	>	for (int l = 0; l <= lMax_;  l++) {
293	>	for (int m = -l; m <= l; m++) {
294	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
295	>	}
296	>	}
297		}
298		}
299	+
300	+	// Normalize Qbar2
301	+	for (int l = 0; l <= lMax_; l++) {
302	+	for (int m = -l; m <= l; m++){
303	+	QBar[std::make_pair(l,m)] /= Nbonds;
304	+	}
305	+	}
306
307	<	// Normalize by number of frames
308	<	for (int m = -lNumber_; m <= lNumber_; m++){
309	<	QBar_lm[m] /=  nFrames;
307	>	// Find second order invariant Q_l
308	>
309	>	for (int l = 0; l <= lMax_; l++) {
310	>	Q2[l] = 0.0;
311	>	for (int m = -l; m <= l; m++){
312	>	Q2[l] += norm(QBar[std::make_pair(l,m)]);
313	>	}
314	>	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
315		}
316
317	<
235	<
236	<
237	<
238	<	writeOrderParameter();
317	>	// Find Third Order Invariant W_l
318
319	+	for (int l = 0; l <= lMax_; l++) {
320	+	W[l] = 0.0;
321	+	for (int m1 = -l; m1 <= l; m1++) {
322	+	std::pair<int,int> lm = std::make_pair(l, m1);
323	+	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
324	+	int m2 = m2Min[lm] + mmm;
325	+	int m3 = -m1-m2;
326	+	W[l] += w3j[lm][mmm] * QBar[lm] *
327	+	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
328	+	}
329	+	}
330	+
331	+	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
332	+	}
333	+
334	+	writeOrderParameter(Q, W_hat);
335		}
336
337	<
338	<	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;
337	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
338	>	std::vector<ComplexType> what) {
339
340	<	for(int i = 0 ; i < histogram_.size(); ++i){
340	>	for (int l = 0; l <= lMax_; l++) {
341	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
342	>	int qbin = (q[l] - MinQ_) / deltaQ_;
343	>	Q_histogram_[std::make_pair(qbin,l)] += 1;
344	>	Qcount_[l]++;
345	>	} else {
346	>	sprintf( painCave.errMsg,
347	>	"q_l value outside reasonable range\n");
348	>	painCave.severity = OPENMD_ERROR;
349	>	painCave.isFatal = 1;
350	>	simError();
351	>	}
352	>	}
353
354	<	RealType rLower = i * deltaR_;
355	<	RealType rUpper = rLower + deltaR_;
356	<	RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
357	<	RealType nIdeal = volSlice * pairConstant;
358	<
359	<	avgGofr_[i] += histogram_[i] / nIdeal;
354	>	for (int l = 0; l <= lMax_; l++) {
355	>	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
356	>	int wbin = (real(what[l]) - MinW_) / deltaW_;
357	>	W_histogram_[std::make_pair(wbin,l)] += 1;
358	>	Wcount_[l]++;
359	>	} else {
360	>	sprintf( painCave.errMsg,
361	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
362	>	painCave.severity = OPENMD_ERROR;
363	>	painCave.isFatal = 1;
364	>	simError();
365	>	}
366		}
367
368	<	}
368	>	}
369
262	–	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
370
371	<	if (Q_l < MaxQ_) {
372	<	int whichBin = Q_l / deltaQ_;
373	<	Q_histogram_[whichBin] += 1;
374	<	}
268	<	if (W_l_hat < MaxW_) {
269	<	int whichBin = W_l_hat / deltaW_;
270	<	W_histogram_[whichBin] += 1;
271	<	}
272	<	}
273	<
371	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
372	>	std::vector<ComplexType> What) {
373	>
374	>	std::ofstream osq((getOutputFileName() + "q").c_str());
375
376	<	void BondOrderParameter::writeOrderParameter() {
376	>	if (osq.is_open()) {
377	>
378	>	osq << "# Bond Order Parameters\n";
379	>	osq << "# selection: (" << selectionScript_ << ")\n";
380	>	osq << "# \n";
381	>	for (int l = 0; l <= lMax_; l++) {
382	>	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
383	>	}
384	>	// Normalize by number of frames and write it out:
385	>	for (int i = 0; i < nBins_; ++i) {
386	>	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
387	>	osq << Qval;
388	>	for (int l = 0; l <= lMax_; l++) {
389
390	<	std::ofstream os(getOutputFileName().c_str());
391	<	os << "#Bond Order Parameter\n";
392	<	os << "#selection: (" << selectionScript_ << ")\n";
390	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
391	>	}
392	>	osq << "\n";
393	>	}
394
395	<	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";
395	>	osq.close();
396
397	+	} else {
398	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
399	+	(getOutputFileName() + "q").c_str());
400	+	painCave.isFatal = 1;
401	+	simError();
402		}
289	–	}
403
404	+	std::ofstream osw((getOutputFileName() + "w").c_str());
405
406	+	if (osw.is_open()) {
407	+	osw << "# Bond Order Parameters\n";
408	+	osw << "# selection: (" << selectionScript_ << ")\n";
409	+	osw << "# \n";
410	+	for (int l = 0; l <= lMax_; l++) {
411	+	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
412	+	}
413	+	// Normalize by number of frames and write it out:
414	+	for (int i = 0; i < nBins_; ++i) {
415	+	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
416	+	osw << Wval;
417	+	for (int l = 0; l <= lMax_; l++) {
418
419	+	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
420	+	}
421	+	osw << "\n";
422	+	}
423	+
424	+	osw.close();
425	+	} else {
426	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
427	+	(getOutputFileName() + "w").c_str());
428	+	painCave.isFatal = 1;
429	+	simError();
430	+	}
431	+
432	+	}
433		}

Comparing:
trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1040 by gezelter, Tue Sep 19 21:20:15 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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