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 |
|
|
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); |
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_ = -0.25; |
86 |
> |
MaxW_ = 0.25; |
87 |
|
deltaW_ = (MaxW_ - MinW_) / nbins; |
88 |
|
} |
89 |
|
|
117 |
|
RealType dist; |
118 |
|
std::map<std::pair<int,int>,ComplexType> q; |
119 |
|
std::vector<RealType> q_l; |
120 |
+ |
std::vector<RealType> q2; |
121 |
+ |
std::vector<ComplexType> w; |
122 |
+ |
std::vector<ComplexType> w_hat; |
123 |
|
std::map<std::pair<int,int>,ComplexType> QBar; |
124 |
|
std::vector<RealType> Q2; |
125 |
|
std::vector<RealType> Q; |
140 |
|
frameCounter_ = 0; |
141 |
|
|
142 |
|
q_l.resize(lMax_+1); |
143 |
+ |
q2.resize(lMax_+1); |
144 |
+ |
w.resize(lMax_+1); |
145 |
+ |
w_hat.resize(lMax_+1); |
146 |
+ |
|
147 |
|
Q2.resize(lMax_+1); |
148 |
|
Q.resize(lMax_+1); |
149 |
|
W.resize(lMax_+1); |
229 |
|
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
230 |
|
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
231 |
|
} |
232 |
< |
collectHistogram(q_l); |
232 |
> |
|
233 |
> |
// Find second order invariant Q_l |
234 |
|
|
235 |
+ |
for (int l = 0; l <= lMax_; l++) { |
236 |
+ |
q2[l] = 0.0; |
237 |
+ |
for (int m = -l; m <= l; m++){ |
238 |
+ |
q2[l] += norm(q[std::make_pair(l,m)]); |
239 |
+ |
} |
240 |
+ |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
241 |
+ |
(RealType)(2*l + 1))/(RealType)nBonds; |
242 |
+ |
} |
243 |
+ |
|
244 |
+ |
// Find Third Order Invariant W_l |
245 |
+ |
|
246 |
+ |
for (int l = 0; l <= lMax_; l++) { |
247 |
+ |
w[l] = 0.0; |
248 |
+ |
lPass = (double)l; |
249 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
250 |
+ |
// Zero work array |
251 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
252 |
+ |
THRCOF[ii] = 0.0; |
253 |
+ |
} |
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 |
+ |
} |
269 |
+ |
} |
270 |
+ |
|
271 |
+ |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
272 |
+ |
} |
273 |
+ |
|
274 |
+ |
collectHistogram(q_l, w_hat); |
275 |
+ |
|
276 |
|
Nbonds += nBonds; |
277 |
|
for (int l = 0; l <= lMax_; l++) { |
278 |
|
for (int m = -l; m <= l; m++) { |
299 |
|
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
300 |
|
} |
301 |
|
|
254 |
– |
|
255 |
– |
|
302 |
|
// Find Third Order Invariant W_l |
303 |
|
|
304 |
|
for (int l = 0; l <= lMax_; l++) { |
332 |
|
writeOrderParameter(Q, W_hat); |
333 |
|
} |
334 |
|
|
335 |
< |
void BondOrderParameter::collectHistogram(std::vector<RealType> q) { |
335 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
336 |
> |
std::vector<ComplexType> what) { |
337 |
|
|
338 |
|
for (int l = 0; l <= lMax_; l++) { |
339 |
|
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
349 |
|
} |
350 |
|
} |
351 |
|
|
352 |
+ |
for (int l = 0; l <= lMax_; l++) { |
353 |
+ |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
354 |
+ |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
355 |
+ |
W_histogram_[std::make_pair(wbin,l)] += 1; |
356 |
+ |
Wcount_[l]++; |
357 |
+ |
} else { |
358 |
+ |
sprintf( painCave.errMsg, |
359 |
+ |
"Re[w_hat] value outside reasonable range\n"); |
360 |
+ |
painCave.severity = OOPSE_ERROR; |
361 |
+ |
painCave.isFatal = 1; |
362 |
+ |
simError(); |
363 |
+ |
} |
364 |
+ |
} |
365 |
+ |
|
366 |
|
} |
367 |
|
|
368 |
|
|
369 |
< |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) { |
369 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
370 |
> |
std::vector<ComplexType> What) { |
371 |
|
|
372 |
< |
std::ofstream os(getOutputFileName().c_str()); |
373 |
< |
|
374 |
< |
if (os.is_open()) { |
372 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
373 |
> |
|
374 |
> |
if (osq.is_open()) { |
375 |
|
|
376 |
< |
os << "# Bond Order Parameters\n"; |
377 |
< |
os << "# selection: (" << selectionScript_ << ")\n"; |
376 |
> |
osq << "# Bond Order Parameters\n"; |
377 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
378 |
> |
osq << "# \n"; |
379 |
|
for (int l = 0; l <= lMax_; l++) { |
380 |
< |
os << "# \n"; |
318 |
< |
os << "# <Q_" << l << ">: " << Q[l] << "\n"; |
319 |
< |
os << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
380 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
381 |
|
} |
382 |
|
// Normalize by number of frames and write it out: |
383 |
|
for (int i = 0; i < nBins_; ++i) { |
384 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
385 |
< |
os << Qval; |
385 |
> |
osq << Qval; |
386 |
|
for (int l = 0; l <= lMax_; l++) { |
387 |
< |
os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
387 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
388 |
|
} |
389 |
< |
os << "\n"; |
389 |
> |
osq << "\n"; |
390 |
|
} |
391 |
|
|
392 |
< |
os.close(); |
392 |
> |
osq.close(); |
393 |
|
|
394 |
|
} else { |
395 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
396 |
< |
getOutputFileName().c_str()); |
396 |
> |
(getOutputFileName() + "q").c_str()); |
397 |
|
painCave.isFatal = 1; |
398 |
|
simError(); |
399 |
|
} |
400 |
+ |
|
401 |
+ |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
402 |
+ |
|
403 |
+ |
if (osw.is_open()) { |
404 |
+ |
osw << "# Bond Order Parameters\n"; |
405 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
406 |
+ |
osw << "# \n"; |
407 |
+ |
for (int l = 0; l <= lMax_; l++) { |
408 |
+ |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
409 |
+ |
} |
410 |
+ |
// Normalize by number of frames and write it out: |
411 |
+ |
for (int i = 0; i < nBins_; ++i) { |
412 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
413 |
+ |
osw << Wval; |
414 |
+ |
for (int l = 0; l <= lMax_; l++) { |
415 |
+ |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l]; |
416 |
+ |
} |
417 |
+ |
osw << "\n"; |
418 |
+ |
} |
419 |
+ |
|
420 |
+ |
osw.close(); |
421 |
+ |
} else { |
422 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
423 |
+ |
(getOutputFileName() + "w").c_str()); |
424 |
+ |
painCave.isFatal = 1; |
425 |
+ |
simError(); |
426 |
+ |
} |
427 |
+ |
|
428 |
|
} |
429 |
|
} |