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

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1049 by gezelter, Fri Sep 22 01:41:11 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 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_ = 3.0;
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> q_lm;
162	<	std::map<int,ComplexType> QBar_lm;
163	<	RealType QSq_l;
164	<	RealType Q_l;
165	<	ComplexType W_l;
166	<	ComplexType W_l_hat;
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;
126	<	// Make arrays for Wigner3jm
127	<	double* THRCOF = new double[mSize_];
128	<	// Variables for Wigner routine
129	<	double l_ = (double)lNumber_;
130	<	double m1Pass, m2Min, m2Max;
131	<	int error, m1, m2, m3;
172	>	int i;
173
133	–	// Set the l for the spherical harmonic, it doesn't change
134	–	sphericalHarmonic.setL(lNumber_);
135	–
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 163 | Line 212 | namespace oopse {
212
213		myIndex = sd->getGlobalIndex();
214		nBonds = 0;
215	<	for (int m = -lNumber_; m <= lNumber_; m++) {
216	<	q_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 177 | 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 191 | 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	<	q_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		}
259		}
260		}
261		}
262	<	RealType ql = 0.0;
263	<	for(int m=-lNumber_; m<=lNumber_; m++) {
264	<	ql += norm(QBar_lm[m]);
265	<	}
266	<	ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1);
267	<	collectHistogram(sqrt(ql)/(RealType)nBonds);
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	>
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	>
274	>	// Find Third Order Invariant W_l
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	>
288	>	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
289	>	}
290
291	+	collectHistogram(q_l, w_hat);
292	+
293		Nbonds += nBonds;
294	<	for (int m=-lNumber_; m<=lNumber_; m++) {
295	<	QBar_lm[m] += q_lm[m];
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	<
301	>
302		// Normalize Qbar2
303	<	for (int m = -lNumber_;m <= lNumber_; m++){
304	<	QBar_lm[m] /= Nbonds;
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		// Find second order invariant Q_l
310
311	<	QSq_l = 0.0;
312	<	for (int m = -lNumber_; m <= lNumber_; m++){
313	<	QSq_l += norm(QBar_lm[m]);
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
230	–	std::cout << "qsl = " << QSq_l << "\n";
231	–	Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1));
232	–
319		// Find Third Order Invariant W_l
320
321	<	W_l = 0.0;
322	<	for (int m1 = -lNumber_; m1 <= lNumber_; m1++) {
323	<	// Zero work array
324	<	for (int ii = 0; ii < mSize_; ii++){
325	<	THRCOF[ii] = 0.0;
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		}
241	–	// Get Wigner coefficients
242	–	m1Pass = (double)m1;
332
333	<	Wigner3jm(&l_, &l_, &l_,
245	<	&m1Pass, &m2Min, &m2Max,
246	<	THRCOF, &mSize_, &error);
247	<
248	<	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
249	<	m2 = (int)floor(m2Min) + mmm;
250	<	m3 = -m1-m2;
251	<	W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3];
252	<	}
333	>	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
334		}
335
336	<	W_l_hat = W_l / pow(QSq_l, 1.5);
256	<
257	<	writeOrderParameter(Q_l, real(W_l_hat));
336	>	writeOrderParameter(Q, W_hat);
337		}
338
339	<	void BondOrderParameter::collectHistogram(RealType q_l) {
339	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340	>	std::vector<ComplexType> what) {
341
342	<	if (q_l >= MinQ_ && q_l < MaxQ_) {
343	<	int qbin = (q_l - MinQ_) / deltaQ_;
344	<	Q_histogram_[qbin] += 1;
345	<	Qcount_++;
346	<	sumQ_ += q_l;
347	<	sumQ2_ += q_l * q_l;
348	<	} else {
349	<	sprintf( painCave.errMsg,
350	<	"q_l value outside reasonable range\n");
351	<	painCave.severity = OOPSE_ERROR;
352	<	painCave.isFatal = 1;
353	<	simError();
342	>	for (int l = 0; l <= lMax_; l++) {
343	>	if (q[l] >= MinQ_ && q[l] < MaxQ_) {
344	>	int qbin = (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	+	for (int l = 0; l <= lMax_; l++) {
357	+	if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) {
358	+	int wbin = (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
372
373	<	void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) {
373	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374	>	std::vector<ComplexType> What) {
375	>
376	>	std::ofstream osq((getOutputFileName() + "q").c_str());
377
378	<	std::ofstream os(getOutputFileName().c_str());
282	<
283	<	if (os.is_open()) {
378	>	if (osq.is_open()) {
379
380	<	os << "# Bond Order Parameters\n";
381	<	os << "# selection: (" << selectionScript_ << ")\n";
382	<	os << "# \n";
383	<	os << "# <Q_" << lNumber_ << ">: " << ql << "\n";
384	<	os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n";
380	>	osq << "# Bond Order Parameters\n";
381	>	osq << "# selection: (" << selectionScript_ << ")\n";
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	<	os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\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
397	<	os.close();
397	>	osq.close();
398
399		} else {
400		sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
401	<	getOutputFileName().c_str());
401	>	(getOutputFileName() + "q").c_str());
402		painCave.isFatal = 1;
403		simError();
404		}
405	+
406	+	std::ofstream osw((getOutputFileName() + "w").c_str());
407	+
408	+	if (osw.is_open()) {
409	+	osw << "# Bond Order Parameters\n";
410	+	osw << "# selection: (" << selectionScript_ << ")\n";
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 < 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	+
426	+	osw.close();
427	+	} else {
428	+	sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n",
429	+	(getOutputFileName() + "w").c_str());
430	+	painCave.isFatal = 1;
431	+	simError();
432	+	}
433	+
434		}
435		}

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords):
Revision 1049 by gezelter, Fri Sep 22 01:41:11 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 0 | Line 1
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