37 |
|
* arising out of the use of or inability to use software, even if the |
38 |
|
* University of Notre Dame has been advised of the possibility of |
39 |
|
* such damages. |
40 |
+ |
* |
41 |
+ |
* BondOrderParameter.cpp |
42 |
+ |
* OOPSE-4 |
43 |
+ |
* |
44 |
+ |
* Created by J. Daniel Gezelter on 09/26/06. |
45 |
+ |
* @author J. Daniel Gezelter |
46 |
+ |
* @version $Id: BondOrderParameter.cpp,v 1.21 2006-11-21 20:44:54 gezelter Exp $ |
47 |
+ |
* |
48 |
|
*/ |
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 |
– |
*/ |
49 |
|
|
50 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
51 |
|
#include "utils/simError.h" |
52 |
|
#include "io/DumpReader.hpp" |
53 |
|
#include "primitives/Molecule.hpp" |
54 |
|
#include "utils/NumericConstant.hpp" |
54 |
– |
#include "math/SphericalHarmonic.hpp" |
55 |
|
|
56 |
|
namespace oopse { |
57 |
|
|
58 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
59 |
|
const std::string& filename, |
60 |
|
const std::string& sele, |
61 |
< |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
61 |
> |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
62 |
|
|
63 |
|
setOutputName(getPrefix(filename) + ".bo"); |
64 |
|
|
69 |
|
|
70 |
|
// Set up cutoff radius and order of the Legendre Polynomial: |
71 |
|
|
72 |
– |
lNumber_ = lNumber; |
72 |
|
rCut_ = rCut; |
73 |
< |
mSize_ = 2*lNumber_+1; |
74 |
< |
} |
73 |
> |
nBins_ = nbins; |
74 |
> |
Qcount_.resize(lMax_+1); |
75 |
> |
Wcount_.resize(lMax_+1); |
76 |
|
|
77 |
+ |
// Q can take values from 0 to 1 |
78 |
+ |
|
79 |
+ |
MinQ_ = 0.0; |
80 |
+ |
MaxQ_ = 1.1; |
81 |
+ |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
82 |
+ |
|
83 |
+ |
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
84 |
+ |
// use values for MinW_ and MaxW_ that are slightly larger than this: |
85 |
+ |
|
86 |
+ |
MinW_ = -0.25; |
87 |
+ |
MaxW_ = 0.25; |
88 |
+ |
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
+ |
|
90 |
+ |
// Make arrays for Wigner3jm |
91 |
+ |
double* THRCOF = new double[2*lMax_+1]; |
92 |
+ |
// Variables for Wigner routine |
93 |
+ |
double lPass, m1Pass, m2m, m2M; |
94 |
+ |
int error, mSize; |
95 |
+ |
mSize = 2*lMax_+1; |
96 |
+ |
|
97 |
+ |
for (int l = 0; l <= lMax_; l++) { |
98 |
+ |
lPass = (double)l; |
99 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
100 |
+ |
m1Pass = (double)m1; |
101 |
+ |
|
102 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
103 |
+ |
|
104 |
+ |
// Zero work array |
105 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
106 |
+ |
THRCOF[ii] = 0.0; |
107 |
+ |
} |
108 |
+ |
|
109 |
+ |
// Get Wigner coefficients |
110 |
+ |
Wigner3jm(&lPass, &lPass, &lPass, |
111 |
+ |
&m1Pass, &m2m, &m2M, |
112 |
+ |
THRCOF, &mSize, &error); |
113 |
+ |
|
114 |
+ |
m2Min[lm] = (int)floor(m2m); |
115 |
+ |
m2Max[lm] = (int)floor(m2M); |
116 |
+ |
|
117 |
+ |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
118 |
+ |
w3j[lm].push_back(THRCOF[mmm]); |
119 |
+ |
} |
120 |
+ |
} |
121 |
+ |
} |
122 |
+ |
delete [] THRCOF; |
123 |
+ |
THRCOF = NULL; |
124 |
+ |
} |
125 |
+ |
|
126 |
|
BondOrderParameter::~BondOrderParameter() { |
127 |
+ |
Q_histogram_.clear(); |
128 |
+ |
W_histogram_.clear(); |
129 |
+ |
for (int l = 0; l <= lMax_; l++) { |
130 |
+ |
for (int m = -l; m <= l; m++) { |
131 |
+ |
w3j[std::make_pair(l,m)].clear(); |
132 |
+ |
} |
133 |
+ |
} |
134 |
+ |
w3j.clear(); |
135 |
+ |
m2Min.clear(); |
136 |
+ |
m2Max.clear(); |
137 |
|
} |
138 |
+ |
|
139 |
+ |
void BondOrderParameter::initalizeHistogram() { |
140 |
+ |
for (int bin = 0; bin < nBins_; bin++) { |
141 |
+ |
for (int l = 0; l <= lMax_; l++) { |
142 |
+ |
Q_histogram_[std::make_pair(bin,l)] = 0; |
143 |
+ |
W_histogram_[std::make_pair(bin,l)] = 0; |
144 |
+ |
} |
145 |
+ |
} |
146 |
+ |
} |
147 |
|
|
148 |
|
void BondOrderParameter::process() { |
149 |
|
Molecule* mol; |
159 |
|
RealType phi; |
160 |
|
RealType r; |
161 |
|
RealType dist; |
162 |
< |
std::map<int,ComplexType> QBar_lm; |
163 |
< |
RealType QSq_l; |
164 |
< |
RealType Q_l; |
165 |
< |
ComplexType W_l; |
166 |
< |
ComplexType W_l_hat; |
167 |
< |
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; |
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_++; |
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; |
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)) |
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 |
|
nBonds++; |
259 |
|
} |
260 |
|
} |
261 |
|
} |
262 |
|
} |
263 |
< |
} |
264 |
< |
} |
263 |
> |
|
264 |
> |
|
265 |
> |
for (int l = 0; l <= lMax_; l++) { |
266 |
> |
q2[l] = 0.0; |
267 |
> |
for (int m = -l; m <= l; m++){ |
268 |
> |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
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], 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)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
297 |
+ |
} |
298 |
+ |
} |
299 |
+ |
} |
300 |
+ |
} |
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 |
|
|
197 |
– |
std::cout << "qsl = " << QSq_l << "\n"; |
198 |
– |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
199 |
– |
|
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 |
|
} |
208 |
– |
// Get Wigner coefficients |
209 |
– |
m1Pass = (double)m1; |
332 |
|
|
333 |
< |
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 |
< |
} |
333 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
334 |
|
} |
335 |
|
|
336 |
< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
223 |
< |
|
224 |
< |
writeOrderParameter(Q_l, real(W_l_hat)); |
336 |
> |
writeOrderParameter(Q, W_hat); |
337 |
|
} |
338 |
|
|
339 |
+ |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
340 |
+ |
std::vector<ComplexType> what) { |
341 |
|
|
342 |
< |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
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 = OOPSE_ERROR; |
351 |
> |
painCave.isFatal = 1; |
352 |
> |
simError(); |
353 |
> |
} |
354 |
> |
} |
355 |
|
|
356 |
< |
std::ofstream os(getOutputFileName().c_str()); |
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 = OOPSE_ERROR; |
365 |
> |
painCave.isFatal = 1; |
366 |
> |
simError(); |
367 |
> |
} |
368 |
> |
} |
369 |
|
|
370 |
< |
if (os.is_open()) { |
370 |
> |
} |
371 |
> |
|
372 |
> |
|
373 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
374 |
> |
std::vector<ComplexType> What) { |
375 |
> |
|
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"; |
382 |
< |
os << "# \n"; |
383 |
< |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
384 |
< |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
385 |
< |
os.close(); |
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 < 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 |
+ |
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 |
|
} |