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root/OpenMD/branches/development/src/applications/staticProps/BondOrderParameter.cpp

Comparing:
trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents), Revision 1052 by gezelter, Tue Sep 26 01:30:32 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 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,
#	Line 82 | 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_ = -0.25;
86	<	MaxW_ = 0.25;
85	>	MinW_ = -1.1;
86	>	MaxW_ = 1.1;
87		deltaW_ = (MaxW_ - MinW_) / nbins;
88	–	}
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	<
137	>
138		void BondOrderParameter::initalizeHistogram() {
139		for (int bin = 0; bin < nBins_; bin++) {
140		for (int l = 0; l <= lMax_; l++) {
#	Line 114 | Line 157 | namespace oopse {
157		RealType costheta;
158		RealType phi;
159		RealType r;
117	–	RealType dist;
160		std::map<std::pair<int,int>,ComplexType> q;
161		std::vector<RealType> q_l;
162		std::vector<RealType> q2;
#	Line 127 | Line 169 | namespace oopse {
169		std::vector<ComplexType> W_hat;
170		int nBonds, Nbonds;
171		SphericalHarmonic sphericalHarmonic;
172	<	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	>	int i;
173
174		DumpReader reader(info_, dumpFilename_);
175		int nFrames = reader.getNFrames();
#	Line 148 | Line 184 | namespace oopse {
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 192 | 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 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		q2[l] += norm(q[std::make_pair(l,m)]);
268		}
269	<	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI /
241	<	(RealType)(2*l + 1))/(RealType)nBonds;
269	>	q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1));
270		}
271	<
271	>
272		// Find Third Order Invariant W_l
273
274		for (int l = 0; l <= lMax_; l++) {
275		w[l] = 0.0;
248	–	lPass = (double)l;
276		for (int m1 = -l; m1 <= l; m1++) {
277	<	// Zero work array
278	<	for (int ii = 0; ii < 2*l + 1; ii++){
279	<	THRCOF[ii] = 0.0;
280	<	}
281	<	// Get Wigner coefficients
282	<	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)];
277	>	std::pair<int,int> lm = std::make_pair(l, m1);
278	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
279	>	int m2 = m2Min[lm] + mmm;
280	>	int m3 = -m1-m2;
281	>	w[l] += w3j[lm][mmm] * q[lm] *
282	>	q[std::make_pair(l,m2)] *  q[std::make_pair(l,m3)];
283		}
284		}
285
286	<	w_hat[l] = w[l] / pow(q2[l], 1.5);
286	>	w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
287		}
288
289		collectHistogram(q_l, w_hat);
#	Line 276 | Line 291 | namespace oopse {
291		Nbonds += nBonds;
292		for (int l = 0; l <= lMax_;  l++) {
293		for (int m = -l; m <= l; m++) {
294	<	QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)];
294	>	QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)];
295		}
296		}
297		}
#	Line 303 | Line 318 | namespace oopse {
318
319		for (int l = 0; l <= lMax_; l++) {
320		W[l] = 0.0;
306	–	lPass = (double)l;
321		for (int m1 = -l; m1 <= l; m1++) {
322	<	// Zero work array
323	<	for (int ii = 0; ii < 2*l + 1; ii++){
324	<	THRCOF[ii] = 0.0;
322	>	std::pair<int,int> lm = std::make_pair(l, m1);
323	>	for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
324	>	int m2 = m2Min[lm] + mmm;
325	>	int m3 = -m1-m2;
326	>	W[l] += w3j[lm][mmm] * QBar[lm] *
327	>	QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)];
328		}
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	–	}
329		}
330
331	<	W_hat[l] = W[l] / pow(Q2[l], 1.5);
331	>	W_hat[l] = W[l] / pow(Q2[l], RealType(1.5));
332		}
333
334		writeOrderParameter(Q, W_hat);
#	Line 343 | Line 345 | namespace oopse {
345		} else {
346		sprintf( painCave.errMsg,
347		"q_l value outside reasonable range\n");
348	<	painCave.severity = OOPSE_ERROR;
348	>	painCave.severity = OPENMD_ERROR;
349		painCave.isFatal = 1;
350		simError();
351		}
#	Line 356 | Line 358 | namespace oopse {
358		Wcount_[l]++;
359		} else {
360		sprintf( painCave.errMsg,
361	<	"Re[w_hat] value outside reasonable range\n");
362	<	painCave.severity = OOPSE_ERROR;
361	>	"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
362	>	painCave.severity = OPENMD_ERROR;
363		painCave.isFatal = 1;
364		simError();
365		}
#	Line 384 | Line 386 | namespace oopse {
386		RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
387		osq << Qval;
388		for (int l = 0; l <= lMax_; l++) {
389	<	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l];
389	>
390	>	osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_;
391		}
392		osq << "\n";
393		}
#	Line 405 | Line 408 | namespace oopse {
408		osw << "# selection: (" << selectionScript_ << ")\n";
409		osw << "# \n";
410		for (int l = 0; l <= lMax_; l++) {
411	<	osw << "# <W_" << l << ">: " << real(What[l]) << "\n";
411	>	osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n";
412		}
413		// Normalize by number of frames and write it out:
414		for (int i = 0; i < nBins_; ++i) {
415		RealType Wval = MinW_ + (i + 0.5) * deltaW_;
416		osw << Wval;
417		for (int l = 0; l <= lMax_; l++) {
418	<	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l];
418	>
419	>	osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_;
420		}
421		osw << "\n";
422		}

Comparing:
trunk/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1052 by gezelter, Tue Sep 26 01:30:32 2006 UTC vs.
branches/development/src/applications/staticProps/BondOrderParameter.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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