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

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1047 by gezelter, Thu Sep 21 21:47:17 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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, 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		*/
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 {
55	<
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)
61	>	: StaticAnalyser(info, filename), selectionScript_(sele), seleMan_(info),
62	>	evaluator_(info) {
63
64		setOutputName(getPrefix(filename) + ".bo");
65
#	Line 69 | Line 70 | namespace oopse {
70
71		// Set up cutoff radius and order of the Legendre Polynomial:
72
72	–	lNumber_ = lNumber;
73		rCut_ = rCut;
74	<	mSize_ = 2*lNumber_+1;
75	<	}
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;
#	Line 90 | Line 159 | namespace oopse {
159		RealType costheta;
160		RealType phi;
161		RealType r;
162	<	RealType dist;
163	<	std::map<int,ComplexType> QBar_lm;
164	<	RealType QSq_l;
165	<	RealType Q_l;
166	<	ComplexType W_l;
167	<	ComplexType W_l_hat;
168	<	int nBonds;
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, j;
102	<	// Make arrays for Wigner3jm
103	<	double* THRCOF = new double[mSize_];
104	<	// Variables for Wigner routine
105	<	double l_ = (double)lNumber_;
106	<	double m1Pass, m2Min, m2Max;
107	<	int error, m1, m2, m3;
174	>	int i;
175
109	–	// Set the l for the spherical harmonic, it doesn't change
110	–	sphericalHarmonic.setL(lNumber_);
111	–
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_++;
#	Line 130 | Line 205 | namespace oopse {
205		rb = mol->nextRigidBody(rbIter)) {
206		rb->updateAtoms();
207		}
208	<	}
209	<
135	<	nBonds = 0;
136	<
137	<	for (int m = -lNumber_; m <= lNumber_; m++) {
138	<	QBar_lm[m] = 0.0;
139	<	}
140	<
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;
#	Line 155 | Line 231 | namespace oopse {
231		if (atom->getGlobalIndex() != myIndex) {
232
233		vec = sd->getPos() - atom->getPos();
234	<	currentSnapshot_->wrapVector(vec);
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))
#	Line 169 | Line 247 | namespace oopse {
247		if (r < rCut_) {
248		costheta = vec.z() / r;
249		phi = atan2(vec.y(), vec.x());
250	<
251	<	for(int m = -lNumber_; m <= lNumber_; m++){
252	<	sphericalHarmonic.setM(m);
253	<	QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi);
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	<	}
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 m = -lNumber_;m <= lNumber_; m++){
306	<	QBar_lm[m] /= nBonds;
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	<	QSq_l = 0.0;
314	<	for (int m = -lNumber_; m <= lNumber_; m++){
315	<	QSq_l += norm(QBar_lm[m]);
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
197	–	std::cout << "qsl = " << QSq_l << "\n";
198	–	Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
199	–
321		// Find Third Order Invariant W_l
322
323	<	W_l = 0.0;
324	<	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
325	<	// Zero work array
326	<	for (int ii = 0; ii < mSize_; ii++){
327	<	THRCOF[ii] = 0.0;
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		}
208	–	// Get Wigner coefficients
209	–	m1Pass = (double)m1;
334
335	<	Wigner3jm(&l_, &l_, &l_,
212	<	&m1Pass, &m2Min, &m2Max,
213	<	THRCOF, &mSize_, &error);
214	<
215	<	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
216	<	m2 = (int)floor(m2Min) + mmm;
217	<	m3 = -m1-m2;
218	<	W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
219	<	}
335	>	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
336		}
337
338	<	W_l_hat = W_l / pow(QSq_l, 1.5);
223	<
224	<	writeOrderParameter(Q_l, real(W_l_hat));
338	>	writeOrderParameter(Q, W_hat);
339		}
340
341	+	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
342	+	std::vector<ComplexType> what) {
343
344	<	void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
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	<	std::ofstream os(getOutputFileName().c_str());
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	<	if (os.is_open()) {
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	<	os << "# Bond Order Parameters\n";
383	<	os << "# selection: (" << selectionScript_ << ")\n";
384	<	os << "# \n";
385	<	os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
386	<	os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
387	<	os.close();
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().c_str());
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 1047 by gezelter, Thu Sep 21 21:47:17 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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