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root/OpenMD/trunk/src/applications/staticProps/BondOrderParameter.cpp

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 994 by chuckv, Tue Jun 27 16:19:28 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 1 | Line 1
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	<	#include "applications/staticProps/P2OrderParameter.hpp"
43	<	#include "utils/simError.h"
44	<	#include "io/DumpReader.hpp"
45	<	#include "primitives/Molecule.hpp"
46	<	#include "utils/NumericConstant.hpp"
47	<	namespace oopse {
48	<
49	<
50	<	P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
51	<	: StaticAnalyser(info, filename),
52	<	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
53	<	seleMan1_(info), seleMan2_(info){
54	<
55	<	setOutputName(getPrefix(filename) + ".p2");
56	<
57	<	evaluator1_.loadScriptString(sele1);
58	<	evaluator2_.loadScriptString(sele2);
59	<
60	<	if (!evaluator1_.isDynamic()) {
61	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
62	<	}else {
63	<	sprintf( painCave.errMsg,
64	<	"--sele1 must be static selection\n");
65	<	painCave.severity = OOPSE_ERROR;
66	<	painCave.isFatal = 1;
67	<	simError();
68	<	}
69	<
70	<	if (!evaluator2_.isDynamic()) {
71	<	seleMan2_.setSelectionSet(evaluator2_.evaluate());
72	<	}else {
73	<	sprintf( painCave.errMsg,
74	<	"--sele2 must be static selection\n");
75	<	painCave.severity = OOPSE_ERROR;
76	<	painCave.isFatal = 1;
77	<	simError();
78	<	}
79	<
80	<	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
81	<	sprintf( painCave.errMsg,
82	<	"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
83	<	painCave.severity = OOPSE_ERROR;
84	<	painCave.isFatal = 1;
85	<	simError();
86	<
87	<	}
88	<
89	<	int i;
90	<	int j;
91	<	StuntDouble* sd1;
92	<	StuntDouble* sd2;
93	<	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
94	<	sd1 != NULL && sd2 != NULL;
95	<	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
96	<
97	<	sdPairs_.push_back(std::make_pair(sd1, sd2));
98	<	}
99	<
100	<
101	<	}
102	<
103	<	void P2OrderParameter::process() {
104	<	Molecule* mol;
105	<	RigidBody* rb;
106	<	SimInfo::MoleculeIterator mi;
107	<	Molecule::RigidBodyIterator rbIter;
108	<
109	<	DumpReader reader(info_, dumpFilename_);
110	<	int nFrames = reader.getNFrames();
111	<
112	<	for (int i = 0; i < nFrames; i += step_) {
113	<	reader.readFrame(i);
114	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
115	<
116	<
117	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
118	<	//change the positions of atoms which belong to the rigidbodies
119	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
120	<	rb->updateAtoms();
121	<	}
122	<
123	<	}
124	<
125	<	Mat3x3d orderTensor(0.0);
126	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
127	<	Vector3d vec = j->first->getPos() - j->second->getPos();
128	<	currentSnapshot_->wrapVector(vec);
129	<	vec.normalize();
130	<	orderTensor +=outProduct(vec, vec);
131	<	}
132	<
133	<	orderTensor /= sdPairs_.size();
134	<	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
135	<
136	<	Vector3d eigenvalues;
137	<	Mat3x3d eigenvectors;
138	<	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
139	<
140	<	int which;
141	<	RealType maxEval = 0.0;
142	<	for(int k = 0; k< 3; k++){
143	<	if(fabs(eigenvalues[k]) > maxEval){
144	<	which = k;
145	<	maxEval = fabs(eigenvalues[k]);
146	<	}
147	<	}
148	<	RealType p2 = 1.5 * maxEval;
149	<
150	<	//the eigen vector is already normalized in SquareMatrix3::diagonalize
151	<	Vector3d director = eigenvectors.getColumn(which);
152	<	if (director[0] < 0) {
153	<	director.negate();
154	<	}
155	<
156	<	RealType angle = 0.0;
157	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
158	<	Vector3d vec = j->first->getPos() - j->second->getPos();
159	<	currentSnapshot_->wrapVector(vec);
160	<	vec.normalize();
161	<
162	<	angle += acos(dot(vec, director)) ;
163	<	}
164	<	angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
165	<
166	<	OrderParam param;
167	<	param.p2 = p2;
168	<	param.director = director;
169	<	param.angle = angle;
170	<
171	<	orderParams_.push_back(param);
172	<
173	<	}
174	<
175	<	writeP2();
176	<
177	<	}
178	<
179	<	void P2OrderParameter::writeP2() {
180	<
181	<	std::ofstream os(getOutputFileName().c_str());
182	<	os << "#radial distribution function\n";
183	<	os<< "#selection1: (" << selectionScript1_ << ")\t";
184	<	os << "selection2: (" << selectionScript2_ << ")\n";
185	<	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
186	<
187	<	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
188	<	os <<  orderParams_[i].p2 << "\t"
189	<	<<  orderParams_[i].director[0] << "\t"
190	<	<<  orderParams_[i].director[1] << "\t"
191	<	<<  orderParams_[i].director[2] << "\t"
192	<	<<  orderParams_[i].angle << "\n";
193	<
194	<	}
195	<
196	<	}
197	<
198	<	}
199	<
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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, 234107 (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	>
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/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 nbins)
61	>	: StaticAnalyser(info, filename), selectionScript_(sele), seleMan_(info),
62	>	evaluator_(info) {
63	>
64	>	setOutputName(getPrefix(filename) + ".bo");
65	>
66	>	evaluator_.loadScriptString(sele);
67	>	if (!evaluator_.isDynamic()) {
68	>	seleMan_.setSelectionSet(evaluator_.evaluate());
69	>	}
70	>
71	>	// Set up cutoff radius and order of the Legendre Polynomial:
72	>
73	>	rCut_ = rCut;
74	>	nBins_ = nbins;
75	>	Qcount_.resize(lMax_+1);
76	>	Wcount_.resize(lMax_+1);
77	>
78	>	// Q can take values from 0 to 1
79	>
80	>	MinQ_ = 0.0;
81	>	MaxQ_ = 1.1;
82	>	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
83	>
84	>	// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
85	>	// use values for MinW_ and MaxW_ that are slightly larger than this:
86	>
87	>	MinW_ = -1.1;
88	>	MaxW_ = 1.1;
89	>	deltaW_ = (MaxW_ - MinW_) / nbins;
90	>
91	>	// Make arrays for Wigner3jm
92	>	RealType* THRCOF = new RealType[2*lMax_+1];
93	>	// Variables for Wigner routine
94	>	RealType lPass, m1Pass, m2m, m2M;
95	>	int error, mSize;
96	>	mSize = 2*lMax_+1;
97	>
98	>	for (int l = 0; l <= lMax_; l++) {
99	>	lPass = (RealType)l;
100	>	for (int m1 = -l; m1 <= l; m1++) {
101	>	m1Pass = (RealType)m1;
102	>
103	>	std::pair<int,int> lm = std::make_pair(l, m1);
104	>
105	>	// Zero work array
106	>	for (int ii = 0; ii < 2*l + 1; ii++){
107	>	THRCOF[ii] = 0.0;
108	>	}
109	>
110	>	// Get Wigner coefficients
111	>	Wigner3jm(lPass, lPass, lPass,
112	>	m1Pass, m2m, m2M,
113	>	THRCOF, mSize, error);
114	>
115	>	m2Min[lm] = (int)floor(m2m);
116	>	m2Max[lm] = (int)floor(m2M);
117	>
118	>	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
119	>	w3j[lm].push_back(THRCOF[mmm]);
120	>	}
121	>	}
122	>	}
123	>	delete [] THRCOF;
124	>	THRCOF = NULL;
125	>	}
126	>
127	>	BondOrderParameter::~BondOrderParameter() {
128	>	Q_histogram_.clear();
129	>	W_histogram_.clear();
130	>	for (int l = 0; l <= lMax_; l++) {
131	>	for (int m = -l; m <= l; m++) {
132	>	w3j[std::make_pair(l,m)].clear();
133	>	}
134	>	}
135	>	w3j.clear();
136	>	m2Min.clear();
137	>	m2Max.clear();
138	>	}
139	>
140	>	void BondOrderParameter::initializeHistogram() {
141	>	for (int bin = 0; bin < nBins_; bin++) {
142	>	for (int l = 0; l <= lMax_; l++) {
143	>	Q_histogram_[std::make_pair(bin,l)] = 0;
144	>	W_histogram_[std::make_pair(bin,l)] = 0;
145	>	}
146	>	}
147	>	}
148	>
149	>	void BondOrderParameter::process() {
150	>	Molecule* mol;
151	>	Atom* atom;
152	>	RigidBody* rb;
153	>	int myIndex;
154	>	SimInfo::MoleculeIterator mi;
155	>	Molecule::RigidBodyIterator rbIter;
156	>	Molecule::AtomIterator ai;
157	>	StuntDouble* sd;
158	>	Vector3d vec;
159	>	RealType costheta;
160	>	RealType phi;
161	>	RealType r;
162	>	std::map<std::pair<int,int>,ComplexType> q;
163	>	std::vector<RealType> q_l;
164	>	std::vector<RealType> q2;
165	>	std::vector<ComplexType> w;
166	>	std::vector<ComplexType> w_hat;
167	>	std::map<std::pair<int,int>,ComplexType> QBar;
168	>	std::vector<RealType> Q2;
169	>	std::vector<RealType> Q;
170	>	std::vector<ComplexType> W;
171	>	std::vector<ComplexType> W_hat;
172	>	int nBonds, Nbonds;
173	>	SphericalHarmonic sphericalHarmonic;
174	>	int i;
175	>
176	>	DumpReader reader(info_, dumpFilename_);
177	>	int nFrames = reader.getNFrames();
178	>	frameCounter_ = 0;
179	>
180	>	q_l.resize(lMax_+1);
181	>	q2.resize(lMax_+1);
182	>	w.resize(lMax_+1);
183	>	w_hat.resize(lMax_+1);
184	>
185	>	Q2.resize(lMax_+1);
186	>	Q.resize(lMax_+1);
187	>	W.resize(lMax_+1);
188	>	W_hat.resize(lMax_+1);
189	>	Nbonds = 0;
190	>
191	>	for (int istep = 0; istep < nFrames; istep += step_) {
192	>	reader.readFrame(istep);
193	>	frameCounter_++;
194	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
195	>
196	>	if (evaluator_.isDynamic()) {
197	>	seleMan_.setSelectionSet(evaluator_.evaluate());
198	>	}
199	>
200	>	// update the positions of atoms which belong to the rigidbodies
201	>
202	>	for (mol = info_->beginMolecule(mi); mol != NULL;
203	>	mol = info_->nextMolecule(mi)) {
204	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
205	>	rb = mol->nextRigidBody(rbIter)) {
206	>	rb->updateAtoms();
207	>	}
208	>	}
209	>
210	>	// outer loop is over the selected StuntDoubles:
211	>
212	>	for (sd = seleMan_.beginSelected(i); sd != NULL;
213	>	sd = seleMan_.nextSelected(i)) {
214	>
215	>	myIndex = sd->getGlobalIndex();
216	>	nBonds = 0;
217	>
218	>	for (int l = 0; l <= lMax_; l++) {
219	>	for (int m = -l; m <= l; m++) {
220	>	q[std::make_pair(l,m)] = 0.0;
221	>	}
222	>	}
223	>
224	>	// inner loop is over all other atoms in the system:
225	>
226	>	for (mol = info_->beginMolecule(mi); mol != NULL;
227	>	mol = info_->nextMolecule(mi)) {
228	>	for (atom = mol->beginAtom(ai); atom != NULL;
229	>	atom = mol->nextAtom(ai)) {
230	>
231	>	if (atom->getGlobalIndex() != myIndex) {
232	>
233	>	vec = sd->getPos() - atom->getPos();
234	>
235	>	if (usePeriodicBoundaryConditions_)
236	>	currentSnapshot_->wrapVector(vec);
237	>
238	>	// Calculate "bonds" and build Q_lm(r) where
239	>	//      Q_lm = Y_lm(theta(r),phi(r))
240	>	// The spherical harmonics are wrt any arbitrary coordinate
241	>	// system, we choose standard spherical coordinates
242	>
243	>	r = vec.length();
244	>
245	>	// Check to see if neighbor is in bond cutoff
246	>
247	>	if (r < rCut_) {
248	>	costheta = vec.z() / r;
249	>	phi = atan2(vec.y(), vec.x());
250	>
251	>	for (int l = 0; l <= lMax_; l++) {
252	>	sphericalHarmonic.setL(l);
253	>	for(int m = -l; m <= l; m++){
254	>	sphericalHarmonic.setM(m);
255	>	q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
256	>
257	>	}
258	>	}
259	>	nBonds++;
260	>	}
261	>	}
262	>	}
263	>	}
264	>
265	>
266	>	for (int l = 0; l <= lMax_; l++) {
267	>	q2[l] = 0.0;
268	>	for (int m = -l; m <= l; m++){
269	>	q[std::make_pair(l,m)] /= (RealType)nBonds;
270	>
271	>	q2[l] += norm(q[std::make_pair(l,m)]);
272	>	}
273	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
274	>	}
275	>
276	>	// Find Third Order Invariant W_l
277	>
278	>	for (int l = 0; l <= lMax_; l++) {
279	>	w[l] = 0.0;
280	>	for (int m1 = -l; m1 <= l; m1++) {
281	>	std::pair<int,int> lm = std::make_pair(l, m1);
282	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
283	>	int m2 = m2Min[lm] + mmm;
284	>	int m3 = -m1-m2;
285	>	w[l] += w3j[lm][mmm] * q[lm] *
286	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
287	>	}
288	>	}
289	>
290	>	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
291	>	}
292	>
293	>	collectHistogram(q_l, w_hat);
294	>
295	>	Nbonds += nBonds;
296	>	for (int l = 0; l <= lMax_;  l++) {
297	>	for (int m = -l; m <= l; m++) {
298	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
299	>	}
300	>	}
301	>	}
302	>	}
303	>
304	>	// Normalize Qbar2
305	>	for (int l = 0; l <= lMax_; l++) {
306	>	for (int m = -l; m <= l; m++){
307	>	QBar[std::make_pair(l,m)] /= Nbonds;
308	>	}
309	>	}
310	>
311	>	// Find second order invariant Q_l
312	>
313	>	for (int l = 0; l <= lMax_; l++) {
314	>	Q2[l] = 0.0;
315	>	for (int m = -l; m <= l; m++){
316	>	Q2[l] += norm(QBar[std::make_pair(l,m)]);
317	>	}
318	>	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
319	>	}
320	>
321	>	// Find Third Order Invariant W_l
322	>
323	>	for (int l = 0; l <= lMax_; l++) {
324	>	W[l] = 0.0;
325	>	for (int m1 = -l; m1 <= l; m1++) {
326	>	std::pair<int,int> lm = std::make_pair(l, m1);
327	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
328	>	int m2 = m2Min[lm] + mmm;
329	>	int m3 = -m1-m2;
330	>	W[l] += w3j[lm][mmm] * QBar[lm] *
331	>	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
332	>	}
333	>	}
334	>
335	>	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
336	>	}
337	>
338	>	writeOrderParameter(Q, W_hat);
339	>	}
340	>
341	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
342	>	std::vector<ComplexType> what) {
343	>
344	>	for (int l = 0; l <= lMax_; l++) {
345	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
346	>	int qbin = int((q[l] - MinQ_) / deltaQ_);
347	>	Q_histogram_[std::make_pair(qbin,l)] += 1;
348	>	Qcount_[l]++;
349	>	} else {
350	>	sprintf( painCave.errMsg,
351	>	"q_l value outside reasonable range\n");
352	>	painCave.severity = OPENMD_ERROR;
353	>	painCave.isFatal = 1;
354	>	simError();
355	>	}
356	>	}
357	>
358	>	for (int l = 0; l <= lMax_; l++) {
359	>	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
360	>	int wbin = int((real(what[l]) - MinW_) / deltaW_);
361	>	W_histogram_[std::make_pair(wbin,l)] += 1;
362	>	Wcount_[l]++;
363	>	} else {
364	>	sprintf( painCave.errMsg,
365	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
366	>	painCave.severity = OPENMD_ERROR;
367	>	painCave.isFatal = 1;
368	>	simError();
369	>	}
370	>	}
371	>
372	>	}
373	>
374	>
375	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
376	>	std::vector<ComplexType> What) {
377	>
378	>	std::ofstream osq((getOutputFileName() + "q").c_str());
379	>
380	>	if (osq.is_open()) {
381	>
382	>	osq << "# Bond Order Parameters\n";
383	>	osq << "# selection: (" << selectionScript_ << ")\n";
384	>	osq << "# \n";
385	>	for (int l = 0; l <= lMax_; l++) {
386	>	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
387	>	}
388	>	// Normalize by number of frames and write it out:
389	>	for (int i = 0; i < nBins_; ++i) {
390	>	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
391	>	osq << Qval;
392	>	for (int l = 0; l <= lMax_; l++) {
393	>
394	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
395	>	}
396	>	osq << "\n";
397	>	}
398	>
399	>	osq.close();
400	>
401	>	} else {
402	>	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
403	>	(getOutputFileName() + "q").c_str());
404	>	painCave.isFatal = 1;
405	>	simError();
406	>	}
407	>
408	>	std::ofstream osw((getOutputFileName() + "w").c_str());
409	>
410	>	if (osw.is_open()) {
411	>	osw << "# Bond Order Parameters\n";
412	>	osw << "# selection: (" << selectionScript_ << ")\n";
413	>	osw << "# \n";
414	>	for (int l = 0; l <= lMax_; l++) {
415	>	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
416	>	}
417	>	// Normalize by number of frames and write it out:
418	>	for (int i = 0; i < nBins_; ++i) {
419	>	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
420	>	osw << Wval;
421	>	for (int l = 0; l <= lMax_; l++) {
422	>
423	>	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
424	>	}
425	>	osw << "\n";
426	>	}
427	>
428	>	osw.close();
429	>	} else {
430	>	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
431	>	(getOutputFileName() + "w").c_str());
432	>	painCave.isFatal = 1;
433	>	simError();
434	>	}
435	>
436	>	}
437	>	}

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords):
Revision 994 by chuckv, Tue Jun 27 16:19:28 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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