71 |
|
|
72 |
|
lNumber_ = lNumber; |
73 |
|
rCut_ = rCut; |
74 |
< |
mSize_ = 2*lNumber_+1; |
74 |
> |
mSize_ = 2*lNumber_+1; |
75 |
|
|
76 |
|
// Q can take values from 0 to 1 |
77 |
|
|
78 |
|
MinQ_ = 0.0; |
79 |
< |
MaxQ_ = 1.0; |
79 |
> |
MaxQ_ = 3.0; |
80 |
|
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
81 |
|
Q_histogram_.resize(nbins); |
82 |
|
|
114 |
|
RealType phi; |
115 |
|
RealType r; |
116 |
|
RealType dist; |
117 |
< |
std::map<int, ComplexType> QBar_lm; |
117 |
> |
std::map<int,ComplexType> q_lm; |
118 |
> |
std::map<int,ComplexType> QBar_lm; |
119 |
|
RealType QSq_l; |
120 |
|
RealType Q_l; |
121 |
|
ComplexType W_l; |
122 |
|
ComplexType W_l_hat; |
123 |
< |
int nBonds; |
123 |
> |
int nBonds, Nbonds; |
124 |
|
SphericalHarmonic sphericalHarmonic; |
125 |
|
int i, j; |
126 |
|
// Make arrays for Wigner3jm |
154 |
|
rb = mol->nextRigidBody(rbIter)) { |
155 |
|
rb->updateAtoms(); |
156 |
|
} |
157 |
< |
} |
158 |
< |
|
157 |
> |
} |
158 |
> |
|
159 |
|
// outer loop is over the selected StuntDoubles: |
160 |
|
|
161 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
162 |
|
sd = seleMan_.nextSelected(i)) { |
163 |
|
|
164 |
|
myIndex = sd->getGlobalIndex(); |
164 |
– |
|
165 |
– |
// For this central atom, zero out nBonds and QBar_lm |
166 |
– |
|
165 |
|
nBonds = 0; |
168 |
– |
|
166 |
|
for (int m = -lNumber_; m <= lNumber_; m++) { |
167 |
< |
QBar_lm[m] = 0.0; |
167 |
> |
q_lm[m] = 0.0; |
168 |
|
} |
169 |
|
|
170 |
|
// inner loop is over all other atoms in the system: |
194 |
|
|
195 |
|
for(int m = -lNumber_; m <= lNumber_; m++){ |
196 |
|
sphericalHarmonic.setM(m); |
197 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
197 |
> |
q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
198 |
|
} |
199 |
|
nBonds++; |
200 |
|
} |
201 |
|
} |
202 |
|
} |
203 |
|
} |
204 |
< |
|
205 |
< |
// Normalize Qbar2 |
206 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
207 |
< |
QBar_lm[m] /= nBonds; |
208 |
< |
std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; |
209 |
< |
} |
204 |
> |
RealType ql = 0.0; |
205 |
> |
for(int m=-lNumber_; m<=lNumber_; m++) { |
206 |
> |
ql += norm(QBar_lm[m]); |
207 |
> |
} |
208 |
> |
ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1); |
209 |
> |
collectHistogram(sqrt(ql)/(RealType)nBonds); |
210 |
|
|
211 |
< |
// Find second order invariant Q_l |
212 |
< |
|
213 |
< |
QSq_l = 0.0; |
217 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
218 |
< |
QSq_l += norm(QBar_lm[m]); |
211 |
> |
Nbonds += nBonds; |
212 |
> |
for (int m=-lNumber_; m<=lNumber_; m++) { |
213 |
> |
QBar_lm[m] += q_lm[m]; |
214 |
|
} |
220 |
– |
std::cout << "qsq_l = " << QSq_l << "\n"; |
221 |
– |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
222 |
– |
|
223 |
– |
// Find Third Order Invariant W_l |
224 |
– |
|
225 |
– |
W_l = 0.0; |
226 |
– |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
227 |
– |
// Zero work array |
228 |
– |
for (int ii = 0; ii < mSize_; ii++){ |
229 |
– |
THRCOF[i] = 0.0; |
230 |
– |
} |
231 |
– |
// Get Wigner coefficients |
232 |
– |
m1Pass = (double)m1; |
233 |
– |
Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
234 |
– |
for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) { |
235 |
– |
m2 = floor(m2Min) + m_index - 1; |
236 |
– |
m3 = -m1-m2; |
237 |
– |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
238 |
– |
} |
239 |
– |
} |
240 |
– |
|
241 |
– |
W_l_hat = W_l / pow(QSq_l, 1.5); |
242 |
– |
|
243 |
– |
// accumulate histogram data for Q_l and W_l_hat: |
244 |
– |
|
245 |
– |
std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; |
246 |
– |
collectHistogram(Q_l, real(W_l_hat)); |
247 |
– |
|
215 |
|
} |
216 |
|
} |
217 |
+ |
|
218 |
+ |
// Normalize Qbar2 |
219 |
+ |
for (int m = -lNumber_;m <= lNumber_; m++){ |
220 |
+ |
QBar_lm[m] /= Nbonds; |
221 |
+ |
} |
222 |
|
|
223 |
< |
writeOrderParameter(); |
223 |
> |
// Find second order invariant Q_l |
224 |
> |
|
225 |
> |
QSq_l = 0.0; |
226 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
227 |
> |
QSq_l += norm(QBar_lm[m]); |
228 |
> |
} |
229 |
> |
|
230 |
> |
std::cout << "qsl = " << QSq_l << "\n"; |
231 |
> |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
232 |
> |
|
233 |
> |
// Find Third Order Invariant W_l |
234 |
> |
|
235 |
> |
W_l = 0.0; |
236 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
237 |
> |
// Zero work array |
238 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
239 |
> |
THRCOF[ii] = 0.0; |
240 |
> |
} |
241 |
> |
// Get Wigner coefficients |
242 |
> |
m1Pass = (double)m1; |
243 |
> |
|
244 |
> |
Wigner3jm(&l_, &l_, &l_, |
245 |
> |
&m1Pass, &m2Min, &m2Max, |
246 |
> |
THRCOF, &mSize_, &error); |
247 |
> |
|
248 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
249 |
> |
m2 = (int)floor(m2Min) + mmm; |
250 |
> |
m3 = -m1-m2; |
251 |
> |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
252 |
> |
} |
253 |
> |
} |
254 |
|
|
255 |
+ |
W_l_hat = W_l / pow(QSq_l, 1.5); |
256 |
+ |
|
257 |
+ |
writeOrderParameter(Q_l, real(W_l_hat)); |
258 |
|
} |
259 |
|
|
260 |
+ |
void BondOrderParameter::collectHistogram(RealType q_l) { |
261 |
|
|
262 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
263 |
< |
|
258 |
< |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
259 |
< |
int qbin = (Q_l - MinQ_) / deltaQ_; |
262 |
> |
if (q_l >= MinQ_ && q_l < MaxQ_) { |
263 |
> |
int qbin = (q_l - MinQ_) / deltaQ_; |
264 |
|
Q_histogram_[qbin] += 1; |
265 |
|
Qcount_++; |
266 |
< |
sumQ_ += Q_l; |
267 |
< |
sumQ2_ += Q_l * Q_l; |
266 |
> |
sumQ_ += q_l; |
267 |
> |
sumQ2_ += q_l * q_l; |
268 |
|
} else { |
269 |
|
sprintf( painCave.errMsg, |
270 |
< |
"Q_l value outside reasonable range\n"); |
270 |
> |
"q_l value outside reasonable range\n"); |
271 |
|
painCave.severity = OOPSE_ERROR; |
272 |
|
painCave.isFatal = 1; |
273 |
|
simError(); |
274 |
|
} |
275 |
|
|
272 |
– |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
273 |
– |
int wbin = (W_l_hat - MinW_) / deltaW_; |
274 |
– |
W_histogram_[wbin] += 1; |
275 |
– |
Wcount_++; |
276 |
– |
sumW_ += W_l_hat; |
277 |
– |
sumW2_ += W_l_hat*W_l_hat; |
278 |
– |
} else { |
279 |
– |
sprintf( painCave.errMsg, |
280 |
– |
"W_l_hat value outside reasonable range\n"); |
281 |
– |
painCave.severity = OOPSE_ERROR; |
282 |
– |
painCave.isFatal = 1; |
283 |
– |
simError(); |
284 |
– |
} |
276 |
|
} |
277 |
|
|
287 |
– |
void BondOrderParameter::writeOrderParameter() { |
278 |
|
|
279 |
< |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
279 |
> |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
280 |
|
|
281 |
< |
if (osq.is_open()) { |
281 |
> |
std::ofstream os(getOutputFileName().c_str()); |
282 |
|
|
283 |
< |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
294 |
< |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
283 |
> |
if (os.is_open()) { |
284 |
|
|
285 |
< |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
286 |
< |
osq << "# selection: (" << selectionScript_ << ")\n"; |
287 |
< |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
288 |
< |
osq << "# std. dev.: " << qStdDev << "\n"; |
289 |
< |
|
285 |
> |
os << "# Bond Order Parameters\n"; |
286 |
> |
os << "# selection: (" << selectionScript_ << ")\n"; |
287 |
> |
os << "# \n"; |
288 |
> |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
289 |
> |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
290 |
|
// Normalize by number of frames and write it out: |
291 |
|
for (int i = 0; i < Q_histogram_.size(); ++i) { |
292 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
293 |
< |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
293 |
> |
os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
294 |
|
} |
306 |
– |
|
307 |
– |
osq.close(); |
308 |
– |
} else { |
309 |
– |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
310 |
– |
(getOutputFileName() + "q").c_str()); |
311 |
– |
painCave.isFatal = 1; |
312 |
– |
simError(); |
313 |
– |
} |
295 |
|
|
296 |
< |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
296 |
> |
os.close(); |
297 |
|
|
317 |
– |
if (osw.is_open()) { |
318 |
– |
|
319 |
– |
RealType wAvg = sumW_ / (RealType) Wcount_; |
320 |
– |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
321 |
– |
|
322 |
– |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
323 |
– |
osw << "# selection: (" << selectionScript_ << ")\n"; |
324 |
– |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
325 |
– |
osw << "# std. dev.: " << wStdDev << "\n"; |
326 |
– |
|
327 |
– |
// Normalize by number of frames and write it out: |
328 |
– |
for (int i = 0; i < W_histogram_.size(); ++i) { |
329 |
– |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
330 |
– |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
331 |
– |
} |
332 |
– |
|
333 |
– |
osw.close(); |
298 |
|
} else { |
299 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
300 |
< |
(getOutputFileName() + "w").c_str()); |
300 |
> |
getOutputFileName().c_str()); |
301 |
|
painCave.isFatal = 1; |
302 |
|
simError(); |
303 |
|
} |