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

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1051 by gezelter, Mon Sep 25 22:08:33 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/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 lMax, 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 68 | Line 68 | namespace oopse {
68
69		// Set up cutoff radius and order of the Legendre Polynomial:
70
71	–	lMax_ = lMax;
71		rCut_ = rCut;
72		nBins_ = nbins;
73		Qcount_.resize(lMax_+1);
#	Line 83 | Line 82 | namespace oopse {
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	–	}
88
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() {
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;
#	Line 115 | Line 157 | namespace oopse {
157		RealType costheta;
158		RealType phi;
159		RealType r;
118	–	RealType dist;
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;
#	Line 125 | Line 169 | namespace oopse {
169		std::vector<ComplexType> W_hat;
170		int nBonds, Nbonds;
171		SphericalHarmonic sphericalHarmonic;
172	<	int i, j;
129	<	// Make arrays for Wigner3jm
130	<	double* THRCOF = new double[2*lMax_+1];
131	<	// Variables for Wigner routine
132	<	double lPass, m1Pass, m2Min, m2Max;
133	<	int error, m1, m2, m3, mSize;
134	<	mSize = 2*lMax_+1;
172	>	int i;
173
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);
#	Line 186 | 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 206 | Line 251 | namespace oopse {
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++;
#	Line 215 | Line 261 | namespace oopse {
261		}
262
263
264	<	for (int l = 0; l <= lMax_; l++) {
265	<	q_l[l] = 0.0;
266	<	for(int m = -l; m <= l; m++) {
267	<	q_l[l] += norm(q[std::make_pair(l,m)]);
268	<	}
269	<	q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
270	<	q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
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		}
226	–	collectHistogram(q_l);
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 l = 0; l <= lMax_;  l++) {
295		for (int m = -l; m <= l; m++) {
296	<	QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
296	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
297		}
298		}
299		}
#	Line 251 | Line 316 | namespace oopse {
316		Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
317		}
318
254	–
255	–
319		// Find Third Order Invariant W_l
320
321		for (int l = 0; l <= lMax_; l++) {
322		W[l] = 0.0;
260	–	lPass = (double)l;
323		for (int m1 = -l; m1 <= l; m1++) {
324	<	// Zero work array
325	<	for (int ii = 0; ii < 2*l + 1; ii++){
326	<	THRCOF[ii] = 0.0;
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		}
266	–	// Get Wigner coefficients
267	–	m1Pass = (double)m1;
268	–
269	–	Wigner3jm(&lPass, &lPass, &lPass,
270	–	&m1Pass, &m2Min, &m2Max,
271	–	THRCOF, &mSize, &error);
272	–
273	–	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
274	–	m2 = (int)floor(m2Min) + mmm;
275	–	m3 = -m1-m2;
276	–	W[l] += THRCOF[mmm] *
277	–	QBar[std::make_pair(l,m1)] *
278	–	QBar[std::make_pair(l,m2)] *
279	–	QBar[std::make_pair(l,m3)];
280	–	}
331		}
332
333	<	W_hat[l] = W[l] / pow(Q2[l], 1.5);
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) {
339	>	void BondOrderParameter::collectHistogram(std::vector<RealType> q,
340	>	std::vector<ComplexType> what) {
341
342		for (int l = 0; l <= lMax_; l++) {
343		if (q[l] >= MinQ_ && q[l] < MaxQ_) {
#	Line 296 | Line 347 | namespace oopse {
347		} else {
348		sprintf( painCave.errMsg,
349		"q_l value outside reasonable range\n");
350	<	painCave.severity = OOPSE_ERROR;
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(std::vector<RealType> Q, std::vector<ComplexType> What) {
373	>	void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q,
374	>	std::vector<ComplexType> What) {
375
376	<	std::ofstream os(getOutputFileName().c_str());
377	<
378	<	if (os.is_open()) {
376	>	std::ofstream osq((getOutputFileName() + "q").c_str());
377	>
378	>	if (osq.is_open()) {
379
380	<	os << "# Bond Order Parameters\n";
381	<	os << "# selection: (" << selectionScript_ << ")\n";
380	>	osq << "# Bond Order Parameters\n";
381	>	osq << "# selection: (" << selectionScript_ << ")\n";
382	>	osq << "# \n";
383		for (int l = 0; l <= lMax_; l++) {
384	<	os << "# \n";
318	<	os << "# <Q_" << l << ">: " << Q[l] << "\n";
319	<	os << "# <W_" << l << ">: " << real(What[l]) << "\n";
384	>	osq << "# <Q_" << l << ">: " << Q[l] << "\n";
385		}
386		// Normalize by number of frames and write it out:
387		for (int i = 0; i < nBins_; ++i) {
388		RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
389	<	os << Qval;
389	>	osq << Qval;
390		for (int l = 0; l <= lMax_; l++) {
391	<	os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
391	>
392	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
393		}
394	<	os << "\n";
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 1051 by gezelter, Mon Sep 25 22:08:33 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 0 | Line 1
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