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

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 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]  Vardeman & Gezelter, in progress (2009).
40	+	*
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"
54	–	#include "math/RealSphericalHarmonic.hpp"
55	–	namespace oopse {
52
53	+	namespace OpenMD {
54
55		BondOrderParameter::BondOrderParameter(SimInfo* info,
56		const std::string& filename,
57		const std::string& sele,
58	<	double rCut, int lNumber, int nbins)
62	<	: StaticAnalyser(info, filename), selectionScript_(sele),
63	<	evaluator_(info), seleMan_(info){
58	>	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
59
60	<	setOutputName(getPrefix(filename) + ".obo");
60	>	setOutputName(getPrefix(filename) + ".bo");
61
62		evaluator_.loadScriptString(sele);
63		if (!evaluator_.isDynamic()) {
#	Line 71 | Line 66 | namespace oopse {
66
67		// Set up cutoff radius and order of the Legendre Polynomial:
68
74	–	lNumber_ = lNumber;
69		rCut_ = rCut;
70	<	mSize_ = 2*lNumber_+1;
70	>	nBins_ = nbins;
71	>	Qcount_.resize(lMax_+1);
72	>	Wcount_.resize(lMax_+1);
73
74	<	// Set the l for the spherical harmonic, it doesn't change
74	>	// Q can take values from 0 to 1
75
76	<	sphericalHarmonic.setL(lNumber_);
76	>	MinQ_ = 0.0;
77	>	MaxQ_ = 1.1;
78	>	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
79
80	<	delta_Q = 1.0 / nbins;
81	<	delta_W = 2.0 / nbins;
80	>	// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
81	>	// use values for MinW_ and MaxW_ that are slightly larger than this:
82
83	<	Q_histogram_.resize(nbins);
84	<	W_histogram_.resize(nbins);
83	>	MinW_ = -1.1;
84	>	MaxW_ = 1.1;
85	>	deltaW_ = (MaxW_ - MinW_) / nbins;
86
87	<	}
87	>	// Make arrays for Wigner3jm
88	>	double* THRCOF = new double[2*lMax_+1];
89	>	// Variables for Wigner routine
90	>	double lPass, m1Pass, m2m, m2M;
91	>	int error, mSize;
92	>	mSize = 2*lMax_+1;
93
94	+	for (int l = 0; l <= lMax_; l++) {
95	+	lPass = (double)l;
96	+	for (int m1 = -l; m1 <= l; m1++) {
97	+	m1Pass = (double)m1;
98	+
99	+	std::pair<int,int> lm = std::make_pair(l, m1);
100	+
101	+	// Zero work array
102	+	for (int ii = 0; ii < 2*l + 1; ii++){
103	+	THRCOF[ii] = 0.0;
104	+	}
105	+
106	+	// Get Wigner coefficients
107	+	Wigner3jm(&lPass, &lPass, &lPass,
108	+	&m1Pass, &m2m, &m2M,
109	+	THRCOF, &mSize, &error);
110	+
111	+	m2Min[lm] = (int)floor(m2m);
112	+	m2Max[lm] = (int)floor(m2M);
113	+
114	+	for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
115	+	w3j[lm].push_back(THRCOF[mmm]);
116	+	}
117	+	}
118	+	}
119	+	delete [] THRCOF;
120	+	THRCOF = NULL;
121	+	}
122	+
123	+	BondOrderParameter::~BondOrderParameter() {
124	+	Q_histogram_.clear();
125	+	W_histogram_.clear();
126	+	for (int l = 0; l <= lMax_; l++) {
127	+	for (int m = -l; m <= l; m++) {
128	+	w3j[std::make_pair(l,m)].clear();
129	+	}
130	+	}
131	+	w3j.clear();
132	+	m2Min.clear();
133	+	m2Max.clear();
134	+	}
135	+
136		void BondOrderParameter::initalizeHistogram() {
137	<	std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
138	<	std::fill(W_histogram_.begin(), W_histogram_.end(), 0);
137	>	for (int bin = 0; bin < nBins_; bin++) {
138	>	for (int l = 0; l <= lMax_; l++) {
139	>	Q_histogram_[std::make_pair(bin,l)] = 0;
140	>	W_histogram_[std::make_pair(bin,l)] = 0;
141	>	}
142	>	}
143		}
144
145		void BondOrderParameter::process() {
146		Molecule* mol;
147		Atom* atom;
148		RigidBody* rb;
149	+	int myIndex;
150		SimInfo::MoleculeIterator mi;
151		Molecule::RigidBodyIterator rbIter;
152		Molecule::AtomIterator ai;
153		StuntDouble* sd;
154	<	RealType theta;
154	>	Vector3d vec;
155	>	RealType costheta;
156		RealType phi;
157		RealType r;
158		RealType dist;
159	<	std::map<int, RealType> QBar_lm;
160	<	RealType QSq_l;
161	<	RealType Q_l;
162	<	int nBonds;
163	<	RealSphericalHarmonic sphericalHarmonic;
159	>	std::map<std::pair<int,int>,ComplexType> q;
160	>	std::vector<RealType> q_l;
161	>	std::vector<RealType> q2;
162	>	std::vector<ComplexType> w;
163	>	std::vector<ComplexType> w_hat;
164	>	std::map<std::pair<int,int>,ComplexType> QBar;
165	>	std::vector<RealType> Q2;
166	>	std::vector<RealType> Q;
167	>	std::vector<ComplexType> W;
168	>	std::vector<ComplexType> W_hat;
169	>	int nBonds, Nbonds;
170	>	SphericalHarmonic sphericalHarmonic;
171		int i, j;
172	<
114	<
172	>
173		DumpReader reader(info_, dumpFilename_);
174		int nFrames = reader.getNFrames();
175	+	frameCounter_ = 0;
176
177	+	q_l.resize(lMax_+1);
178	+	q2.resize(lMax_+1);
179	+	w.resize(lMax_+1);
180	+	w_hat.resize(lMax_+1);
181
182	+	Q2.resize(lMax_+1);
183	+	Q.resize(lMax_+1);
184	+	W.resize(lMax_+1);
185	+	W_hat.resize(lMax_+1);
186	+	Nbonds = 0;
187	+
188		for (int istep = 0; istep < nFrames; istep += step_) {
189		reader.readFrame(istep);
190	+	frameCounter_++;
191		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
192
193		if (evaluator_.isDynamic()) {
#	Line 132 | Line 202 | namespace oopse {
202		rb = mol->nextRigidBody(rbIter)) {
203		rb->updateAtoms();
204		}
205	<	}
206	<
205	>	}
206	>
207		// outer loop is over the selected StuntDoubles:
208
209		for (sd = seleMan_.beginSelected(i); sd != NULL;
210		sd = seleMan_.nextSelected(i)) {
211
212	<	// For this central atom, zero out nBonds and QBar_lm
143	<
212	>	myIndex = sd->getGlobalIndex();
213		nBonds = 0;
214	<
215	<	for (int m = -lNumber_; m <= lNumber_; m++) {
216	<	QBar_lm[m] = 0.0;
214	>
215	>	for (int l = 0; l <= lMax_; l++) {
216	>	for (int m = -l; m <= l; m++) {
217	>	q[std::make_pair(l,m)] = 0.0;
218	>	}
219		}
220
221		// inner loop is over all other atoms in the system:
#	Line 154 | Line 225 | namespace oopse {
225		for (atom = mol->beginAtom(ai); atom != NULL;
226		atom = mol->nextAtom(ai)) {
227
228	+	if (atom->getGlobalIndex() != myIndex) {
229
230	<	Vector3d vec = sd->getPos() - atom->getPos();
231	<	currentSnapshot_->wrapVector(vec);
232	<
233	<	// Calculate "bonds" and build Q_lm(r) where
234	<	//      Q_lm = Y_lm(theta(r),phi(r))
235	<	// The spherical harmonics are wrt any arbitrary coordinate
236	<	// system, we choose standard spherical coordinates
237	<
238	<	r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
239	<
240	<	// Check to see if neighbor is in bond cutoff
241	<
242	<	if (r < rCut_) {
243	<	theta = atan2(vec.y(), vec.x());
244	<	phi = acos(vec.z()/r);
245	<	for(int m = -lNumber_; m <= lNumber_; m++){
246	<	sphericalHarmonic.setM(m);
247	<	QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi);
248	<	}
249	<	nBonds++;
250	<	}
230	>	vec = sd->getPos() - atom->getPos();
231	>
232	>	if (usePeriodicBoundaryConditions_)
233	>	currentSnapshot_->wrapVector(vec);
234	>
235	>	// Calculate "bonds" and build Q_lm(r) where
236	>	//      Q_lm = Y_lm(theta(r),phi(r))
237	>	// The spherical harmonics are wrt any arbitrary coordinate
238	>	// system, we choose standard spherical coordinates
239	>
240	>	r = vec.length();
241	>
242	>	// Check to see if neighbor is in bond cutoff
243	>
244	>	if (r < rCut_) {
245	>	costheta = vec.z() / r;
246	>	phi = atan2(vec.y(), vec.x());
247	>
248	>	for (int l = 0; l <= lMax_; l++) {
249	>	sphericalHarmonic.setL(l);
250	>	for(int m = -l; m <= l; m++){
251	>	sphericalHarmonic.setM(m);
252	>	q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi);
253	>	}
254	>	}
255	>	nBonds++;
256	>	}
257	>	}
258		}
259		}
260
261	<	// Normalize Qbar
262	<	for (int m = -lNumber_;m <= lNumber_; m++){
263	<	QBar_lm[m] /= nBonds;
261	>
262	>	for (int l = 0; l <= lMax_; l++) {
263	>	q2[l] = 0.0;
264	>	for (int m = -l; m <= l; m++){
265	>	q[std::make_pair(l,m)] /= (RealType)nBonds;
266	>	q2[l] += norm(q[std::make_pair(l,m)]);
267	>	}
268	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
269		}
270	<
187	<	// Find second order invariant Q_l
188	<
189	<	QSq_l = 0.0;
190	<	for (int m = -lNumber_; m <= lNumber_; m++){
191	<	QSq_l += pow(QBar_lm[m], 2);
192	<	}
193	<	Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
194	<
270	>
271		// Find Third Order Invariant W_l
272	+
273	+	for (int l = 0; l <= lMax_; l++) {
274	+	w[l] = 0.0;
275	+	for (int m1 = -l; m1 <= l; m1++) {
276	+	std::pair<int,int> lm = std::make_pair(l, m1);
277	+	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
278	+	int m2 = m2Min[lm] + mmm;
279	+	int m3 = -m1-m2;
280	+	w[l] += w3j[lm][mmm] * q[lm] *
281	+	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
282	+	}
283	+	}
284	+
285	+	w_hat[l] = w[l] / pow(q2[l], 1.5);
286	+	}
287
288	<	// Make arrays for Wigner3jm
198	<	double* THRCOF = new double[mSize_];
199	<	// Variables for Wigner routine
200	<	double l_ = (double)lNumber_;
201	<	double m2Min, m2Max;
202	<	int error, m1, m2, m3;
288	>	collectHistogram(q_l, w_hat);
289
290	<	W_l_ = 0.0;
291	<	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
292	<	// Zero work array
293	<	for (int ii = 0; ii < mSize_; ii+){
208	<	THRCOF[i] = 0.0;
290	>	Nbonds += nBonds;
291	>	for (int l = 0; l <= lMax_;  l++) {
292	>	for (int m = -l; m <= l; m++) {
293	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
294		}
210	–	// Get Wigner coefficients
211	–	Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error);
212	–	for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) {
213	–	m2 = floor(m2Min) + m_index - 1;
214	–	m3 = -m1-m2;
215	–	W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
216	–	}
295		}
218	–
219	–	W_l_hat = W_l_ / pow(QSq_l, 1.5);
220	–
221	–	// accumulate histogram data for Q_l and W_l_hat:
222	–
223	–	collectHistogram(Q_l, W_l_hat);
224	–
296		}
297		}
298	+
299	+	// Normalize Qbar2
300	+	for (int l = 0; l <= lMax_; l++) {
301	+	for (int m = -l; m <= l; m++){
302	+	QBar[std::make_pair(l,m)] /= Nbonds;
303	+	}
304	+	}
305
306	<	// Normalize by number of frames
307	<	for (int m = -lNumber_; m <= lNumber_; m++){
308	<	QBar_lm[m] /=  nFrames;
306	>	// Find second order invariant Q_l
307	>
308	>	for (int l = 0; l <= lMax_; l++) {
309	>	Q2[l] = 0.0;
310	>	for (int m = -l; m <= l; m++){
311	>	Q2[l] += norm(QBar[std::make_pair(l,m)]);
312	>	}
313	>	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
314		}
315
316	<
234	<
235	<
236	<
237	<	writeOrderParameter();
316	>	// Find Third Order Invariant W_l
317
318	+	for (int l = 0; l <= lMax_; l++) {
319	+	W[l] = 0.0;
320	+	for (int m1 = -l; m1 <= l; m1++) {
321	+	std::pair<int,int> lm = std::make_pair(l, m1);
322	+	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
323	+	int m2 = m2Min[lm] + mmm;
324	+	int m3 = -m1-m2;
325	+	W[l] += w3j[lm][mmm] * QBar[lm] *
326	+	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
327	+	}
328	+	}
329	+
330	+	W_hat[l] = W[l] / pow(Q2[l], 1.5);
331	+	}
332	+
333	+	writeOrderParameter(Q, W_hat);
334		}
335
336	<
337	<	void BondOrderParameter::processHistogram() {
243	<
244	<	int nPairs = getNPairs();
245	<	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
246	<	RealType pairDensity = nPairs /volume * 2.0;
247	<	RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
336	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
337	>	std::vector<ComplexType> what) {
338
339	<	for(int i = 0 ; i < histogram_.size(); ++i){
339	>	for (int l = 0; l <= lMax_; l++) {
340	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
341	>	int qbin = (q[l] - MinQ_) / deltaQ_;
342	>	Q_histogram_[std::make_pair(qbin,l)] += 1;
343	>	Qcount_[l]++;
344	>	} else {
345	>	sprintf( painCave.errMsg,
346	>	"q_l value outside reasonable range\n");
347	>	painCave.severity = OPENMD_ERROR;
348	>	painCave.isFatal = 1;
349	>	simError();
350	>	}
351	>	}
352
353	<	RealType rLower = i * deltaR_;
354	<	RealType rUpper = rLower + deltaR_;
355	<	RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
356	<	RealType nIdeal = volSlice * pairConstant;
357	<
358	<	avgGofr_[i] += histogram_[i] / nIdeal;
353	>	for (int l = 0; l <= lMax_; l++) {
354	>	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
355	>	int wbin = (real(what[l]) - MinW_) / deltaW_;
356	>	W_histogram_[std::make_pair(wbin,l)] += 1;
357	>	Wcount_[l]++;
358	>	} else {
359	>	sprintf( painCave.errMsg,
360	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
361	>	painCave.severity = OPENMD_ERROR;
362	>	painCave.isFatal = 1;
363	>	simError();
364	>	}
365		}
366
367	<	}
367	>	}
368
261	–	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
369
370	<	if (Q_l < Max_Q) {
371	<	int whichBin = Q_l / deltaQ_;
372	<	Q_histogram_[whichBin] += 1;
373	<	}
267	<	if (W_l_hat < Max_W) {
268	<	int whichBin = W_l_hat / deltaW_;
269	<	W_histogram_[whichBin] += 1;
270	<	}
271	<	}
272	<
370	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
371	>	std::vector<ComplexType> What) {
372	>
373	>	std::ofstream osq((getOutputFileName() + "q").c_str());
374
375	<	void BondOrderParameter::writeOrderParameter() {
375	>	if (osq.is_open()) {
376	>
377	>	osq << "# Bond Order Parameters\n";
378	>	osq << "# selection: (" << selectionScript_ << ")\n";
379	>	osq << "# \n";
380	>	for (int l = 0; l <= lMax_; l++) {
381	>	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
382	>	}
383	>	// Normalize by number of frames and write it out:
384	>	for (int i = 0; i < nBins_; ++i) {
385	>	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
386	>	osq << Qval;
387	>	for (int l = 0; l <= lMax_; l++) {
388
389	<	std::ofstream os(getOutputFileName().c_str());
390	<	os << "#Bond Order Parameter\n";
391	<	os << "#selection: (" << selectionScript_ << ")\n";
389	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
390	>	}
391	>	osq << "\n";
392	>	}
393
394	<	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
281	<	os <<  orderParams_[i].p2 << "\t"
282	<	<<  orderParams_[i].director[0] << "\t"
283	<	<<  orderParams_[i].director[1] << "\t"
284	<	<<  orderParams_[i].director[2] << "\t"
285	<	<<  orderParams_[i].angle << "\n";
394	>	osq.close();
395
396	+	} else {
397	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
398	+	(getOutputFileName() + "q").c_str());
399	+	painCave.isFatal = 1;
400	+	simError();
401		}
288	–	}
402
403	+	std::ofstream osw((getOutputFileName() + "w").c_str());
404
405	+	if (osw.is_open()) {
406	+	osw << "# Bond Order Parameters\n";
407	+	osw << "# selection: (" << selectionScript_ << ")\n";
408	+	osw << "# \n";
409	+	for (int l = 0; l <= lMax_; l++) {
410	+	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
411	+	}
412	+	// Normalize by number of frames and write it out:
413	+	for (int i = 0; i < nBins_; ++i) {
414	+	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
415	+	osw << Wval;
416	+	for (int l = 0; l <= lMax_; l++) {
417
418	+	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
419	+	}
420	+	osw << "\n";
421	+	}
422	+
423	+	osw.close();
424	+	} else {
425	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
426	+	(getOutputFileName() + "w").c_str());
427	+	painCave.isFatal = 1;
428	+	simError();
429	+	}
430	+
431	+	}
432		}

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords):
Revision 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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