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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1052 by gezelter, Tue Sep 26 01:30:32 2006 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 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"
#	Line 52 | Line 50
50		#include "primitives/Molecule.hpp"
51		#include "utils/NumericConstant.hpp"
52
53	<	namespace oopse {
53	>	namespace OpenMD {
54
55		BondOrderParameter::BondOrderParameter(SimInfo* info,
56		const std::string& filename,
#	Line 82 | Line 80 | namespace oopse {
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	<	MinW_ = -0.25;
84	<	MaxW_ = 0.25;
83	>	MinW_ = -1.1;
84	>	MaxW_ = 1.1;
85		deltaW_ = (MaxW_ - MinW_) / nbins;
88	–	}
86
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	<
135	>
136		void BondOrderParameter::initalizeHistogram() {
137		for (int bin = 0; bin < nBins_; bin++) {
138		for (int l = 0; l <= lMax_; l++) {
#	Line 128 | Line 169 | namespace oopse {
169		int nBonds, Nbonds;
170		SphericalHarmonic sphericalHarmonic;
171		int i, j;
131	–	// Make arrays for Wigner3jm
132	–	double* THRCOF = new double[2*lMax_+1];
133	–	// Variables for Wigner routine
134	–	double lPass, m1Pass, m2Min, m2Max;
135	–	int error, m1, m2, m3, mSize;
136	–	mSize = 2*lMax_+1;
172
173		DumpReader reader(info_, dumpFilename_);
174		int nFrames = reader.getNFrames();
#	Line 148 | Line 183 | namespace oopse {
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);
#	Line 192 | Line 228 | namespace oopse {
228		if (atom->getGlobalIndex() != myIndex) {
229
230		vec = sd->getPos() - atom->getPos();
231	<	currentSnapshot_->wrapVector(vec);
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))
#	Line 212 | Line 250 | namespace oopse {
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		}
256		nBonds++;
#	Line 221 | Line 260 | namespace oopse {
260		}
261
262
224	–	for (int l = 0; l <= lMax_; l++) {
225	–	q_l[l] = 0.0;
226	–	for(int m = -l; m <= l; m++) {
227	–	q_l[l] += norm(q[std::make_pair(l,m)]);
228	–	}
229	–	q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1);
230	–	q_l[l] = sqrt(q_l[l])/(RealType)nBonds;
231	–	}
232	–
233	–	// Find second order invariant Q_l
234	–
263		for (int l = 0; l <= lMax_; l++) {
264		q2[l] = 0.0;
265		for (int m = -l; m <= l; m++){
266	+	q[std::make_pair(l,m)] /= (RealType)nBonds;
267	+
268		q2[l] += norm(q[std::make_pair(l,m)]);
269		}
270	<	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241	<	(RealType)(2*l + 1))/(RealType)nBonds;
270	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
271		}
272	<
272	>
273		// Find Third Order Invariant W_l
274
275		for (int l = 0; l <= lMax_; l++) {
276		w[l] = 0.0;
248	–	lPass = (double)l;
277		for (int m1 = -l; m1 <= l; m1++) {
278	<	// Zero work array
279	<	for (int ii = 0; ii < 2*l + 1; ii++){
280	<	THRCOF[ii] = 0.0;
278	>	std::pair<int,int> lm = std::make_pair(l, m1);
279	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
280	>	int m2 = m2Min[lm] + mmm;
281	>	int m3 = -m1-m2;
282	>	w[l] += w3j[lm][mmm] * q[lm] *
283	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
284		}
254	–	// Get Wigner coefficients
255	–	m1Pass = (double)m1;
256	–
257	–	Wigner3jm(&lPass, &lPass, &lPass,
258	–	&m1Pass, &m2Min, &m2Max,
259	–	THRCOF, &mSize, &error);
260	–
261	–	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
262	–	m2 = (int)floor(m2Min) + mmm;
263	–	m3 = -m1-m2;
264	–	w[l] += THRCOF[mmm] *
265	–	q[std::make_pair(l,m1)] *
266	–	q[std::make_pair(l,m2)] *
267	–	q[std::make_pair(l,m3)];
268	–	}
285		}
286
287		w_hat[l] = w[l] / pow(q2[l], 1.5);
#	Line 276 | Line 292 | namespace oopse {
292		Nbonds += nBonds;
293		for (int l = 0; l <= lMax_;  l++) {
294		for (int m = -l; m <= l; m++) {
295	<	QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
295	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
296		}
297		}
298		}
#	Line 303 | Line 319 | namespace oopse {
319
320		for (int l = 0; l <= lMax_; l++) {
321		W[l] = 0.0;
306	–	lPass = (double)l;
322		for (int m1 = -l; m1 <= l; m1++) {
323	<	// Zero work array
324	<	for (int ii = 0; ii < 2*l + 1; ii++){
325	<	THRCOF[ii] = 0.0;
323	>	std::pair<int,int> lm = std::make_pair(l, m1);
324	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
325	>	int m2 = m2Min[lm] + mmm;
326	>	int m3 = -m1-m2;
327	>	W[l] += w3j[lm][mmm] * QBar[lm] *
328	>	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
329		}
312	–	// Get Wigner coefficients
313	–	m1Pass = (double)m1;
314	–
315	–	Wigner3jm(&lPass, &lPass, &lPass,
316	–	&m1Pass, &m2Min, &m2Max,
317	–	THRCOF, &mSize, &error);
318	–
319	–	for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) {
320	–	m2 = (int)floor(m2Min) + mmm;
321	–	m3 = -m1-m2;
322	–	W[l] += THRCOF[mmm] *
323	–	QBar[std::make_pair(l,m1)] *
324	–	QBar[std::make_pair(l,m2)] *
325	–	QBar[std::make_pair(l,m3)];
326	–	}
330		}
331
332		W_hat[l] = W[l] / pow(Q2[l], 1.5);
#	Line 343 | Line 346 | namespace oopse {
346		} else {
347		sprintf( painCave.errMsg,
348		"q_l value outside reasonable range\n");
349	<	painCave.severity = OOPSE_ERROR;
349	>	painCave.severity = OPENMD_ERROR;
350		painCave.isFatal = 1;
351		simError();
352		}
#	Line 356 | Line 359 | namespace oopse {
359		Wcount_[l]++;
360		} else {
361		sprintf( painCave.errMsg,
362	<	"Re[w_hat] value outside reasonable range\n");
363	<	painCave.severity = OOPSE_ERROR;
362	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
363	>	painCave.severity = OPENMD_ERROR;
364		painCave.isFatal = 1;
365		simError();
366		}
#	Line 384 | Line 387 | namespace oopse {
387		RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
388		osq << Qval;
389		for (int l = 0; l <= lMax_; l++) {
390	<	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
390	>
391	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
392		}
393		osq << "\n";
394		}
#	Line 405 | Line 409 | namespace oopse {
409		osw << "# selection: (" << selectionScript_ << ")\n";
410		osw << "# \n";
411		for (int l = 0; l <= lMax_; l++) {
412	<	osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
412	>	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
413		}
414		// Normalize by number of frames and write it out:
415		for (int i = 0; i < nBins_; ++i) {
416		RealType Wval = MinW_ + (i + 0.5) * deltaW_;
417		osw << Wval;
418		for (int l = 0; l <= lMax_; l++) {
419	<	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
419	>
420	>	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
421		}
422		osw << "\n";
423		}

Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords):
Revision 1052 by gezelter, Tue Sep 26 01:30:32 2006 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

#	Line 0 | Line 1
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