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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 1038 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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		*/
46	<
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	<
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, const std::string& filename, const std::string& sele1,
58	<	const std::string& sele2, double rCut, int lNumber)
59	<	: StaticAnalyser(info, filename),
60	<	selectionScript1_(sele1), evaluator1_(info),
61	<	seleMan1_(info){
57	>	BondOrderParameter::BondOrderParameter(SimInfo* info,
58	>	const std::string& filename,
59	>	const std::string& sele,
60	>	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61	>
62	>	setOutputName(getPrefix(filename) + ".bo");
63
64	<	setOutputName(getPrefix(filename) + ".obo");
65	<
66	<	evaluator1_.loadScriptString(sele1);
67	<	evaluator2_.loadScriptString(sele2);
68	<
69	<	if (!evaluator1_.isDynamic()) {
70	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
71	<	}else {
72	<	sprintf( painCave.errMsg,
73	<	"--sele1 must be static selection\n");
74	<	painCave.severity = OOPSE_ERROR;
75	<	painCave.isFatal = 1;
76	<	simError();
64	>	evaluator_.loadScriptString(sele);
65	>	if (!evaluator_.isDynamic()) {
66	>	seleMan_.setSelectionSet(evaluator_.evaluate());
67		}
68
69	<	/* Set up cutoff radius and type of order parameter we are calcuating*/
70	<	lNumber_ = lNumber;
69	>	// Set up cutoff radius and order of the Legendre Polynomial:
70	>
71		rCut_ = rCut;
72	<	mSize_ = 2*lNumber_+1;
72	>	nBins_ = nbins;
73	>	Qcount_.resize(lMax_+1);
74	>	Wcount_.resize(lMax_+1);
75
76	<	int i;
85	<	int j;
86	<	StuntDouble* sd1;
87	<	StuntDouble* sd2;
88	<	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
89	<	sd1 != NULL && sd2 != NULL;
90	<	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
91	<	for (sd2 = seleMan1_.beginSelected(j),sd2
92	<	sdPairs_.push_back(std::make_pair(sd1, sd2));
93	<	}
76	>	// Q can take values from 0 to 1
77
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	<	void BondOrderParameter::process
86	<	() {
87	<	Molecule* mol;
101	<	RigidBody* rb;
102	<	SimInfo::MoleculeIterator mi;
103	<	Molecule::RigidBodyIterator rbIter;
104	<	RealType theta;
105	<	RealType phi;
106	<	RealType r;
107	<	RealType dist;
108	<	RealType* QBar_lm;
109	<	RealType QSq_l;
110	<	int nBonds;
111	<	int m, m_index;
112	<	RealSphericalHarmonic sphericalHarmonic;
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	<	DumpReader reader(info_, dumpFilename_);
97	<	int nFrames = reader.getNFrames();
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	<	/*Set the l for the spherical harmonic, it doesn't change*/
102	<	sphericalHarmonic.setL(lNumber_);
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	<	for (int i = 0; i < nFrames; i += step_) {
109	<	reader.readFrame(i);
110	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
111	<	nBonds = 0;
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	>	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	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
148	<	//change the positions of atoms which belong to the rigidbodies
149	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
150	<	rb->updateAtoms();
151	<	}
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	>	Vector3d vec;
157	>	RealType costheta;
158	>	RealType phi;
159	>	RealType r;
160	>	RealType dist;
161	>	std::map<std::pair<int,int>,ComplexType> q;
162	>	std::vector<RealType> q_l;
163	>	std::vector<RealType> q2;
164	>	std::vector<ComplexType> w;
165	>	std::vector<ComplexType> w_hat;
166	>	std::map<std::pair<int,int>,ComplexType> QBar;
167	>	std::vector<RealType> Q2;
168	>	std::vector<RealType> Q;
169	>	std::vector<ComplexType> W;
170	>	std::vector<ComplexType> W_hat;
171	>	int nBonds, Nbonds;
172	>	SphericalHarmonic sphericalHarmonic;
173	>	int i, j;
174
175	<	}
175	>	DumpReader reader(info_, dumpFilename_);
176	>	int nFrames = reader.getNFrames();
177	>	frameCounter_ = 0;
178
179	+	q_l.resize(lMax_+1);
180	+	q2.resize(lMax_+1);
181	+	w.resize(lMax_+1);
182	+	w_hat.resize(lMax_+1);
183
184	<	/* Setup QBar */
185	<	QBar_lm = new double[mSize_];
184	>	Q2.resize(lMax_+1);
185	>	Q.resize(lMax_+1);
186	>	W.resize(lMax_+1);
187	>	W_hat.resize(lMax_+1);
188	>	Nbonds = 0;
189
190	<	/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
191	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
192	<	Vector3d vec = j->first->getPos() - j->second->getPos();
193	<	currentSnapshot_->wrapVector(vec);
194	<	/* The spherical harmonics are wrt any arbitray coordiate sysetm,
195	<	* we choose standard spherical coordinates */
196	<	r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
190	>	for (int istep = 0; istep < nFrames; istep += step_) {
191	>	reader.readFrame(istep);
192	>	frameCounter_++;
193	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
194	>
195	>	if (evaluator_.isDynamic()) {
196	>	seleMan_.setSelectionSet(evaluator_.evaluate());
197	>	}
198
199	<	/* Check to see if neighbor is in bond cuttoff*/
147	<	if (r<rCut_){
148	<	theta = atan(vec.y()/vec.x());
149	<	phi = acos(vec.z()/r);
150	<	for(int m_index = 0; m_index < mSize_; m_index++){
151	<	sphericalHarmonic.setM(m_index-lNumber_);
152	<	QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi);
153	<	}
154	<	nBonds++;
155	<	}
156	<	}
199	>	// update the positions of atoms which belong to the rigidbodies
200
201	<	/*Normalize Qbar by number of Bonds*/
202	<	for ( int m_index = 0;m_index < mSize_; m_index++){
203	<	QBar_lm(m_index) = QBar_lm(m_index)/nBonds;
204	<	}
201	>	for (mol = info_->beginMolecule(mi); mol != NULL;
202	>	mol = info_->nextMolecule(mi)) {
203	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
204	>	rb = mol->nextRigidBody(rbIter)) {
205	>	rb->updateAtoms();
206	>	}
207	>	}
208	>
209	>	// outer loop is over the selected StuntDoubles:
210
211	+	for (sd = seleMan_.beginSelected(i); sd != NULL;
212	+	sd = seleMan_.nextSelected(i)) {
213
214	<	}
214	>	myIndex = sd->getGlobalIndex();
215	>	nBonds = 0;
216	>
217	>	for (int l = 0; l <= lMax_; l++) {
218	>	for (int m = -l; m <= l; m++) {
219	>	q[std::make_pair(l,m)] = 0.0;
220	>	}
221	>	}
222	>
223	>	// inner loop is over all other atoms in the system:
224	>
225	>	for (mol = info_->beginMolecule(mi); mol != NULL;
226	>	mol = info_->nextMolecule(mi)) {
227	>	for (atom = mol->beginAtom(ai); atom != NULL;
228	>	atom = mol->nextAtom(ai)) {
229
230	<	/*Normalize by number of frames*/
167	<	for ( int m_index = 0;m_index < mSize_; m_index++){
168	<	QBar_lm(m_index) = QBar_lm(m_index)/nFrames;
169	<	}
230	>	if (atom->getGlobalIndex() != myIndex) {
231
232	+	vec = sd->getPos() - atom->getPos();
233
234	+	if (usePeriodicBoundaryConditions_)
235	+	currentSnapshot_->wrapVector(vec);
236	+
237	+	// Calculate "bonds" and build Q_lm(r) where
238	+	//      Q_lm = Y_lm(theta(r),phi(r))
239	+	// The spherical harmonics are wrt any arbitrary coordinate
240	+	// system, we choose standard spherical coordinates
241	+
242	+	r = vec.length();
243	+
244	+	// Check to see if neighbor is in bond cutoff
245	+
246	+	if (r < rCut_) {
247	+	costheta = vec.z() / r;
248	+	phi = atan2(vec.y(), vec.x());
249
250	<	/* Find second order invariant Q_l*/
250	>	for (int l = 0; l <= lMax_; l++) {
251	>	sphericalHarmonic.setL(l);
252	>	for(int m = -l; m <= l; m++){
253	>	sphericalHarmonic.setM(m);
254	>	q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
255	>	}
256	>	}
257	>	nBonds++;
258	>	}
259	>	}
260	>	}
261	>	}
262	>
263	>
264	>	for (int l = 0; l <= lMax_; l++) {
265	>	q2[l] = 0.0;
266	>	for (int m = -l; m <= l; m++){
267	>	q[std::make_pair(l,m)] /= (RealType)nBonds;
268	>	q2[l] += norm(q[std::make_pair(l,m)]);
269	>	}
270	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
271	>	}
272	>
273	>	// Find Third Order Invariant W_l
274	>
275	>	for (int l = 0; l <= lMax_; l++) {
276	>	w[l] = 0.0;
277	>	for (int m1 = -l; m1 <= l; m1++) {
278	>	std::pair<int,int> lm = std::make_pair(l, m1);
279	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
280	>	int m2 = m2Min[lm] + mmm;
281	>	int m3 = -m1-m2;
282	>	w[l] += w3j[lm][mmm] * q[lm] *
283	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
284	>	}
285	>	}
286	>
287	>	w_hat[l] = w[l] / pow(q2[l], 1.5);
288	>	}
289
290	<	for (int m_index = 0 ;m_index <= sizeM_; m++){
291	<	QSq_l += pow(QBar_lm(m),2);
290	>	collectHistogram(q_l, w_hat);
291	>
292	>	Nbonds += nBonds;
293	>	for (int l = 0; l <= lMax_;  l++) {
294	>	for (int m = -l; m <= l; m++) {
295	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
296	>	}
297	>	}
298		}
299	<	Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
299	>	}
300	>
301	>	// Normalize Qbar2
302	>	for (int l = 0; l <= lMax_; l++) {
303	>	for (int m = -l; m <= l; m++){
304	>	QBar[std::make_pair(l,m)] /= Nbonds;
305	>	}
306	>	}
307	>
308	>	// Find second order invariant Q_l
309	>
310	>	for (int l = 0; l <= lMax_; l++) {
311	>	Q2[l] = 0.0;
312	>	for (int m = -l; m <= l; m++){
313	>	Q2[l] += norm(QBar[std::make_pair(l,m)]);
314	>	}
315	>	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
316	>	}
317	>
318	>	// Find Third Order Invariant W_l
319	>
320	>	for (int l = 0; l <= lMax_; l++) {
321	>	W[l] = 0.0;
322	>	for (int m1 = -l; m1 <= l; m1++) {
323	>	std::pair<int,int> lm = std::make_pair(l, m1);
324	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
325	>	int m2 = m2Min[lm] + mmm;
326	>	int m3 = -m1-m2;
327	>	W[l] += w3j[lm][mmm] * QBar[lm] *
328	>	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
329	>	}
330	>	}
331	>
332	>	W_hat[l] = W[l] / pow(Q2[l], 1.5);
333	>	}
334	>
335	>	writeOrderParameter(Q, W_hat);
336	>	}
337
338	<	/* Find Third Order Invariant W_l*/
338	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
339	>	std::vector<ComplexType> what) {
340
341	<	/* Make arrays for Wigner3jm */
342	<	double* THRCOF = new double[mSize_];
343	<	/* Variables for Wigner routine */
344	<	double l_ = (double)lNumber_;
345	<	double m2Min;
346	<	double m2Max;
347	<	int error;
348	<	int m1;
349	<	int m2;
350	<	int m3;
341	>	for (int l = 0; l <= lMax_; l++) {
342	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
343	>	int qbin = (q[l] - MinQ_) / deltaQ_;
344	>	Q_histogram_[std::make_pair(qbin,l)] += 1;
345	>	Qcount_[l]++;
346	>	} else {
347	>	sprintf( painCave.errMsg,
348	>	"q_l value outside reasonable range\n");
349	>	painCave.severity = OPENMD_ERROR;
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>	}
354
355	<	for (int m1 = -lNumber_;m <= lNumber_;m1++){
356	<	/* Zero work array */
357	<	for (i=0; i<mSize_;i++){
358	<	THRCOF[i] = 0.0;
359	<	}
360	<	/* Get wigner coefficients */
361	<	Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error);
362	<	for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){
363	<	m2 = floor(m2Min) + m_index - 1;
364	<	m3 = -m1-m2;
365	<	W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_);
204	<	}
355	>	for (int l = 0; l <= lMax_; l++) {
356	>	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
357	>	int wbin = (real(what[l]) - MinW_) / deltaW_;
358	>	W_histogram_[std::make_pair(wbin,l)] += 1;
359	>	Wcount_[l]++;
360	>	} else {
361	>	sprintf( painCave.errMsg,
362	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
363	>	painCave.severity = OPENMD_ERROR;
364	>	painCave.isFatal = 1;
365	>	simError();
366		}
367	+	}
368
369	+	}
370
208	–	writeOrderParameter();
371
372	<	}
372	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
373	>	std::vector<ComplexType> What) {
374	>
375	>	std::ofstream osq((getOutputFileName() + "q").c_str());
376
377	+	if (osq.is_open()) {
378	+
379	+	osq << "# Bond Order Parameters\n";
380	+	osq << "# selection: (" << selectionScript_ << ")\n";
381	+	osq << "# \n";
382	+	for (int l = 0; l <= lMax_; l++) {
383	+	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
384	+	}
385	+	// Normalize by number of frames and write it out:
386	+	for (int i = 0; i < nBins_; ++i) {
387	+	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
388	+	osq << Qval;
389	+	for (int l = 0; l <= lMax_; l++) {
390
391	<	void BondOrderParameter::writeOrderParameter() {
391	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
392	>	}
393	>	osq << "\n";
394	>	}
395
396	<	std::ofstream os(getOutputFileName().c_str());
216	<	os << "#radial distribution function\n";
217	<	os<< "#selection1: (" << selectionScript1_ << ")\t";
218	<	os << "selection2: (" << selectionScript2_ << ")\n";
219	<	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
396	>	osq.close();
397
398	<	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
399	<	os <<  orderParams_[i].p2 << "\t"
400	<	<<  orderParams_[i].director[0] << "\t"
401	<	<<  orderParams_[i].director[1] << "\t"
402	<	<<  orderParams_[i].director[2] << "\t"
403	<	<<  orderParams_[i].angle << "\n";
398	>	} else {
399	>	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
400	>	(getOutputFileName() + "q").c_str());
401	>	painCave.isFatal = 1;
402	>	simError();
403	>	}
404
405	+	std::ofstream osw((getOutputFileName() + "w").c_str());
406	+
407	+	if (osw.is_open()) {
408	+	osw << "# Bond Order Parameters\n";
409	+	osw << "# selection: (" << selectionScript_ << ")\n";
410	+	osw << "# \n";
411	+	for (int l = 0; l <= lMax_; l++) {
412	+	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
413		}
414	+	// Normalize by number of frames and write it out:
415	+	for (int i = 0; i < nBins_; ++i) {
416	+	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
417	+	osw << Wval;
418	+	for (int l = 0; l <= lMax_; l++) {
419
420	<	}
420	>	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
421	>	}
422	>	osw << "\n";
423	>	}
424
425	+	osw.close();
426	+	} else {
427	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
428	+	(getOutputFileName() + "w").c_str());
429	+	painCave.isFatal = 1;
430	+	simError();
431	+	}
432	+
433		}
434	<
434	>	}

Comparing:
trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1038 by chuckv, Mon Sep 18 21:31:23 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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