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

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1043 by gezelter, Thu Sep 21 14:45:08 2006 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 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/SphericalHarmonic.hpp"
52	>	#include "math/Wigner3jm.hpp"
53
54	<	namespace oopse {
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) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
60	>	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
61
62		setOutputName(getPrefix(filename) + ".bo");
63
#	Line 69 | Line 68 | namespace oopse {
68
69		// Set up cutoff radius and order of the Legendre Polynomial:
70
72	–	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		// Q can take values from 0 to 1
77
78		MinQ_ = 0.0;
79	<	MaxQ_ = 1.0;
79	>	MaxQ_ = 1.1;
80		deltaQ_ = (MaxQ_ - MinQ_) / nbins;
81	–	Q_histogram_.resize(nbins);
81
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_ = -0.18;
86	<	MaxW_ = 0.18;
85	>	MinW_ = -1.1;
86	>	MaxW_ = 1.1;
87		deltaW_ = (MaxW_ - MinW_) / nbins;
89	–	W_histogram_.resize(nbins);
88
89	<	}
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);
137	>
138	>	void BondOrderParameter::initializeHistogram() {
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() {
#	Line 113 | Line 157 | namespace oopse {
157		RealType costheta;
158		RealType phi;
159		RealType r;
160	<	RealType dist;
161	<	std::map<int, ComplexType> QBar_lm;
162	<	RealType QSq_l;
163	<	RealType Q_l;
164	<	ComplexType W_l;
165	<	ComplexType W_l_hat;
166	<	int nBonds;
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, j;
125	<	// Make arrays for Wigner3jm
126	<	double* THRCOF = new double[mSize_];
127	<	// Variables for Wigner routine
128	<	double l_ = (double)lNumber_;
129	<	double m1Pass, m2Min, m2Max;
130	<	int error, m1, m2, m3;
172	>	int i;
173
132	–	// Set the l for the spherical harmonic, it doesn't change
133	–	sphericalHarmonic.setL(lNumber_);
134	–
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_++;
#	Line 153 | 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		myIndex = sd->getGlobalIndex();
164	–
165	–	// For this central atom, zero out nBonds and QBar_lm
166	–
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 180 | Line 229 | namespace oopse {
229		if (atom->getGlobalIndex() != myIndex) {
230
231		vec = sd->getPos() - atom->getPos();
232	<	currentSnapshot_->wrapVector(vec);
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))
#	Line 194 | Line 245 | namespace oopse {
245		if (r < rCut_) {
246		costheta = vec.z() / r;
247		phi = atan2(vec.y(), vec.x());
248	<
249	<	for(int m = -lNumber_; m <= lNumber_; m++){
250	<	sphericalHarmonic.setM(m);
251	<	QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi);
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		}
257		nBonds++;
258		}
#	Line 205 | Line 260 | namespace oopse {
260		}
261		}
262
263	<	// Normalize Qbar2
264	<	for (int m = -lNumber_;m <= lNumber_; m++){
265	<	QBar_lm[m] /= nBonds;
266	<	std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n";
267	<	}
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
269	<	// Find second order invariant Q_l
270	<
271	<	QSq_l = 0.0;
217	<	for (int m = -lNumber_; m <= lNumber_; m++){
218	<	QSq_l += norm(QBar_lm[m]);
269	>	q2[l] += norm(q[std::make_pair(l,m)]);
270	>	}
271	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
272		}
273	<	std::cout << "qsq_l = " << QSq_l << "\n";
221	<	Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1)));
222	<
273	>
274		// Find Third Order Invariant W_l
275	<
276	<	W_l = 0.0;
277	<	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
278	<	// Zero work array
279	<	for (int ii = 0; ii < mSize_; ii++){
280	<	THRCOF[i] = 0.0;
275	>
276	>	for (int l = 0; l <= lMax_; l++) {
277	>	w[l] = 0.0;
278	>	for (int m1 = -l; m1 <= l; m1++) {
279	>	std::pair<int,int> lm = std::make_pair(l, m1);
280	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
281	>	int m2 = m2Min[lm] + mmm;
282	>	int m3 = -m1-m2;
283	>	w[l] += w3j[lm][mmm] * q[lm] *
284	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
285	>	}
286		}
287	<	// Get Wigner coefficients
288	<	m1Pass = (double)m1;
233	<	Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error);
234	<	for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) {
235	<	m2 = floor(m2Min) + m_index - 1;
236	<	m3 = -m1-m2;
237	<	W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_];
238	<	}
287	>
288	>	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
289		}
240	–
241	–	W_l_hat = W_l / pow(QSq_l, 1.5);
242	–
243	–	// accumulate histogram data for Q_l and W_l_hat:
290
291	<	std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n";
292	<	collectHistogram(Q_l, real(W_l_hat));
293	<
291	>	collectHistogram(q_l, w_hat);
292	>
293	>	Nbonds += nBonds;
294	>	for (int l = 0; l <= lMax_;  l++) {
295	>	for (int m = -l; m <= l; m++) {
296	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
297	>	}
298	>	}
299		}
300		}
301	+
302	+	// Normalize Qbar2
303	+	for (int l = 0; l <= lMax_; l++) {
304	+	for (int m = -l; m <= l; m++){
305	+	QBar[std::make_pair(l,m)] /= Nbonds;
306	+	}
307	+	}
308
309	<	writeOrderParameter();
309	>	// Find second order invariant Q_l
310
311	+	for (int l = 0; l <= lMax_; l++) {
312	+	Q2[l] = 0.0;
313	+	for (int m = -l; m <= l; m++){
314	+	Q2[l] += norm(QBar[std::make_pair(l,m)]);
315	+	}
316	+	Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317	+	}
318	+
319	+	// Find Third Order Invariant W_l
320	+
321	+	for (int l = 0; l <= lMax_; l++) {
322	+	W[l] = 0.0;
323	+	for (int m1 = -l; m1 <= l; m1++) {
324	+	std::pair<int,int> lm = std::make_pair(l, m1);
325	+	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
326	+	int m2 = m2Min[lm] + mmm;
327	+	int m3 = -m1-m2;
328	+	W[l] += w3j[lm][mmm] * QBar[lm] *
329	+	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
330	+	}
331	+	}
332	+
333	+	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
334	+	}
335	+
336	+	writeOrderParameter(Q, W_hat);
337		}
338
339	+	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340	+	std::vector<ComplexType> what) {
341
342	<	void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) {
343	<
344	<	if (Q_l >= MinQ_ && Q_l < MaxQ_) {
345	<	int qbin = (Q_l - MinQ_) / deltaQ_;
346	<	Q_histogram_[qbin] += 1;
347	<	Qcount_++;
348	<	sumQ_ += Q_l;
349	<	sumQ2_ += Q_l * Q_l;
350	<	} else {
351	<	sprintf( painCave.errMsg,
352	<	"Q_l value outside reasonable range\n");
353	<	painCave.severity = OOPSE_ERROR;
268	<	painCave.isFatal = 1;
269	<	simError();
342	>	for (int l = 0; l <= lMax_; l++) {
343	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344	>	int qbin = int((q[l] - MinQ_) / deltaQ_);
345	>	Q_histogram_[std::make_pair(qbin,l)] += 1;
346	>	Qcount_[l]++;
347	>	} else {
348	>	sprintf( painCave.errMsg,
349	>	"q_l value outside reasonable range\n");
350	>	painCave.severity = OPENMD_ERROR;
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354		}
355
356	<	if (W_l_hat >= MinW_ && W_l_hat < MaxW_) {
357	<	int wbin = (W_l_hat - MinW_) / deltaW_;
358	<	W_histogram_[wbin] += 1;
359	<	Wcount_++;
360	<	sumW_  += W_l_hat;
361	<	sumW2_ += W_l_hat*W_l_hat;
362	<	} else {
363	<	sprintf( painCave.errMsg,
364	<	"W_l_hat value outside reasonable range\n");
365	<	painCave.severity = OOPSE_ERROR;
366	<	painCave.isFatal = 1;
367	<	simError();
356	>	for (int l = 0; l <= lMax_; l++) {
357	>	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358	>	int wbin = int((real(what[l]) - MinW_) / deltaW_);
359	>	W_histogram_[std::make_pair(wbin,l)] += 1;
360	>	Wcount_[l]++;
361	>	} else {
362	>	sprintf( painCave.errMsg,
363	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
364	>	painCave.severity = OPENMD_ERROR;
365	>	painCave.isFatal = 1;
366	>	simError();
367	>	}
368		}
369	+
370		}
371
287	–	void BondOrderParameter::writeOrderParameter() {
372
373	+	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374	+	std::vector<ComplexType> What) {
375	+
376		std::ofstream osq((getOutputFileName() + "q").c_str());
377
378		if (osq.is_open()) {
292	–
293	–	RealType qAvg = sumQ_ / (RealType) Qcount_;
294	–	RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg;
379
380	<	osq << "# Bond Order Parameter Q_" << lNumber_ << "\n";
380	>	osq << "# Bond Order Parameters\n";
381		osq << "# selection: (" << selectionScript_ << ")\n";
382	<	osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n";
383	<	osq << "# std. dev.: " << qStdDev << "\n";
384	<
382	>	osq << "# \n";
383	>	for (int l = 0; l <= lMax_; l++) {
384	>	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385	>	}
386		// Normalize by number of frames and write it out:
387	<	for (int i = 0; i < Q_histogram_.size(); ++i) {
388	<	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
389	<	osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n";
387	>	for (int i = 0; i < nBins_; ++i) {
388	>	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
389	>	osq << Qval;
390	>	for (int l = 0; l <= lMax_; l++) {
391	>
392	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393	>	}
394	>	osq << "\n";
395		}
396	<
396	>
397		osq.close();
398	+
399		} else {
400		sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401		(getOutputFileName() + "q").c_str());
#	Line 315 | Line 406 | namespace oopse {
406		std::ofstream osw((getOutputFileName() + "w").c_str());
407
408		if (osw.is_open()) {
409	<
319	<	RealType wAvg = sumW_ / (RealType) Wcount_;
320	<	RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg;
321	<
322	<	osw << "# Bond Order Parameter W_" << lNumber_ << "\n";
409	>	osw << "# Bond Order Parameters\n";
410		osw << "# selection: (" << selectionScript_ << ")\n";
411	<	osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n";
412	<	osw << "# std. dev.: " << wStdDev << "\n";
413	<
411	>	osw << "# \n";
412	>	for (int l = 0; l <= lMax_; l++) {
413	>	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
414	>	}
415		// Normalize by number of frames and write it out:
416	<	for (int i = 0; i < W_histogram_.size(); ++i) {
417	<	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
418	<	osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n";
416	>	for (int i = 0; i < nBins_; ++i) {
417	>	RealType Wval = MinW_ + (i + 0.5) * deltaW_;
418	>	osw << Wval;
419	>	for (int l = 0; l <= lMax_; l++) {
420	>
421	>	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
422	>	}
423	>	osw << "\n";
424		}
425	<
425	>
426		osw.close();
427		} else {
428		sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
#	Line 337 | Line 430 | namespace oopse {
430		painCave.isFatal = 1;
431		simError();
432		}
433	+
434		}
435		}

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords):
Revision 1043 by gezelter, Thu Sep 21 14:45:08 2006 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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