51 |
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#include "io/DumpReader.hpp" |
52 |
|
#include "primitives/Molecule.hpp" |
53 |
|
#include "utils/NumericConstant.hpp" |
54 |
– |
#include "math/SphericalHarmonic.hpp" |
54 |
|
|
55 |
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namespace oopse { |
56 |
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|
57 |
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
58 |
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const std::string& filename, |
59 |
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const std::string& sele, |
60 |
< |
double rCut, int lNumber, 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 |
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|
62 |
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setOutputName(getPrefix(filename) + ".bo"); |
63 |
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|
68 |
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|
69 |
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// Set up cutoff radius and order of the Legendre Polynomial: |
70 |
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|
72 |
– |
lNumber_ = lNumber; |
71 |
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rCut_ = rCut; |
72 |
< |
mSize_ = 2*lNumber_+1; |
72 |
> |
nBins_ = nbins; |
73 |
> |
Qcount_.resize(lMax_+1); |
74 |
> |
Wcount_.resize(lMax_+1); |
75 |
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|
76 |
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// Q can take values from 0 to 1 |
77 |
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|
78 |
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MinQ_ = 0.0; |
79 |
< |
MaxQ_ = 3.0; |
79 |
> |
MaxQ_ = 1.1; |
80 |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
81 |
– |
Q_histogram_.resize(nbins); |
81 |
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|
82 |
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
83 |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
84 |
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|
85 |
< |
MinW_ = -0.18; |
86 |
< |
MaxW_ = 0.18; |
85 |
> |
MinW_ = -0.25; |
86 |
> |
MaxW_ = 0.25; |
87 |
|
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
– |
W_histogram_.resize(nbins); |
90 |
– |
|
88 |
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} |
89 |
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|
90 |
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BondOrderParameter::~BondOrderParameter() { |
93 |
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} |
94 |
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|
95 |
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void BondOrderParameter::initalizeHistogram() { |
96 |
< |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
97 |
< |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
96 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
97 |
> |
for (int l = 0; l <= lMax_; l++) { |
98 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
99 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
100 |
> |
} |
101 |
> |
} |
102 |
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} |
103 |
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|
104 |
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void BondOrderParameter::process() { |
115 |
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RealType phi; |
116 |
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RealType r; |
117 |
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RealType dist; |
118 |
< |
std::map<int,ComplexType> q_lm; |
119 |
< |
std::map<int,ComplexType> QBar_lm; |
120 |
< |
RealType QSq_l; |
121 |
< |
RealType Q_l; |
122 |
< |
ComplexType W_l; |
123 |
< |
ComplexType W_l_hat; |
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; |
126 |
> |
std::vector<ComplexType> W; |
127 |
> |
std::vector<ComplexType> W_hat; |
128 |
|
int nBonds, Nbonds; |
129 |
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SphericalHarmonic sphericalHarmonic; |
130 |
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int i, j; |
131 |
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// Make arrays for Wigner3jm |
132 |
< |
double* THRCOF = new double[mSize_]; |
132 |
> |
double* THRCOF = new double[2*lMax_+1]; |
133 |
|
// Variables for Wigner routine |
134 |
< |
double l_ = (double)lNumber_; |
135 |
< |
double m1Pass, m2Min, m2Max; |
136 |
< |
int error, m1, m2, m3; |
134 |
> |
double lPass, m1Pass, m2Min, m2Max; |
135 |
> |
int error, m1, m2, m3, mSize; |
136 |
> |
mSize = 2*lMax_+1; |
137 |
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|
133 |
– |
// Set the l for the spherical harmonic, it doesn't change |
134 |
– |
sphericalHarmonic.setL(lNumber_); |
135 |
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|
138 |
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DumpReader reader(info_, dumpFilename_); |
139 |
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int nFrames = reader.getNFrames(); |
140 |
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frameCounter_ = 0; |
141 |
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|
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); |
150 |
+ |
W_hat.resize(lMax_+1); |
151 |
+ |
|
152 |
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for (int istep = 0; istep < nFrames; istep += step_) { |
153 |
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reader.readFrame(istep); |
154 |
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frameCounter_++; |
175 |
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|
176 |
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myIndex = sd->getGlobalIndex(); |
177 |
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nBonds = 0; |
178 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
179 |
< |
q_lm[m] = 0.0; |
178 |
> |
|
179 |
> |
for (int l = 0; l <= lMax_; l++) { |
180 |
> |
for (int m = -l; m <= l; m++) { |
181 |
> |
q[std::make_pair(l,m)] = 0.0; |
182 |
> |
} |
183 |
|
} |
184 |
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|
185 |
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// inner loop is over all other atoms in the system: |
206 |
|
if (r < rCut_) { |
207 |
|
costheta = vec.z() / r; |
208 |
|
phi = atan2(vec.y(), vec.x()); |
209 |
< |
|
210 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
211 |
< |
sphericalHarmonic.setM(m); |
212 |
< |
q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
209 |
> |
|
210 |
> |
for (int l = 0; l <= lMax_; l++) { |
211 |
> |
sphericalHarmonic.setL(l); |
212 |
> |
for(int m = -l; m <= l; m++){ |
213 |
> |
sphericalHarmonic.setM(m); |
214 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
215 |
> |
} |
216 |
|
} |
217 |
|
nBonds++; |
218 |
|
} |
219 |
|
} |
220 |
|
} |
221 |
|
} |
222 |
< |
RealType ql = 0.0; |
223 |
< |
for(int m=-lNumber_; m<=lNumber_; m++) { |
224 |
< |
ql += norm(QBar_lm[m]); |
225 |
< |
} |
226 |
< |
ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1); |
227 |
< |
collectHistogram(sqrt(ql)/(RealType)nBonds); |
222 |
> |
|
223 |
> |
|
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 |
+ |
|
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 m=-lNumber_; m<=lNumber_; m++) { |
278 |
< |
QBar_lm[m] += q_lm[m]; |
277 |
> |
for (int l = 0; l <= lMax_; l++) { |
278 |
> |
for (int m = -l; m <= l; m++) { |
279 |
> |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
280 |
> |
} |
281 |
|
} |
282 |
|
} |
283 |
|
} |
284 |
< |
|
284 |
> |
|
285 |
|
// Normalize Qbar2 |
286 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
287 |
< |
QBar_lm[m] /= Nbonds; |
286 |
> |
for (int l = 0; l <= lMax_; l++) { |
287 |
> |
for (int m = -l; m <= l; m++){ |
288 |
> |
QBar[std::make_pair(l,m)] /= Nbonds; |
289 |
> |
} |
290 |
|
} |
291 |
|
|
292 |
|
// Find second order invariant Q_l |
293 |
|
|
294 |
< |
QSq_l = 0.0; |
295 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
296 |
< |
QSq_l += norm(QBar_lm[m]); |
294 |
> |
for (int l = 0; l <= lMax_; l++) { |
295 |
> |
Q2[l] = 0.0; |
296 |
> |
for (int m = -l; m <= l; m++){ |
297 |
> |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
298 |
> |
} |
299 |
> |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
300 |
|
} |
229 |
– |
|
230 |
– |
std::cout << "qsl = " << QSq_l << "\n"; |
231 |
– |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
301 |
|
|
302 |
|
// Find Third Order Invariant W_l |
303 |
|
|
304 |
< |
W_l = 0.0; |
305 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
306 |
< |
// Zero work array |
307 |
< |
for (int ii = 0; ii < mSize_; ii++){ |
308 |
< |
THRCOF[ii] = 0.0; |
304 |
> |
for (int l = 0; l <= lMax_; l++) { |
305 |
> |
W[l] = 0.0; |
306 |
> |
lPass = (double)l; |
307 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
308 |
> |
// Zero work array |
309 |
> |
for (int ii = 0; ii < 2*l + 1; ii++){ |
310 |
> |
THRCOF[ii] = 0.0; |
311 |
> |
} |
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 |
> |
} |
327 |
|
} |
241 |
– |
// Get Wigner coefficients |
242 |
– |
m1Pass = (double)m1; |
328 |
|
|
329 |
< |
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 |
< |
} |
329 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
330 |
|
} |
331 |
|
|
332 |
< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
256 |
< |
|
257 |
< |
writeOrderParameter(Q_l, real(W_l_hat)); |
332 |
> |
writeOrderParameter(Q, W_hat); |
333 |
|
} |
334 |
|
|
335 |
< |
void BondOrderParameter::collectHistogram(RealType q_l) { |
335 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
336 |
> |
std::vector<ComplexType> what) { |
337 |
|
|
338 |
< |
if (q_l >= MinQ_ && q_l < MaxQ_) { |
339 |
< |
int qbin = (q_l - MinQ_) / deltaQ_; |
340 |
< |
Q_histogram_[qbin] += 1; |
341 |
< |
Qcount_++; |
342 |
< |
sumQ_ += q_l; |
343 |
< |
sumQ2_ += q_l * q_l; |
344 |
< |
} else { |
345 |
< |
sprintf( painCave.errMsg, |
346 |
< |
"q_l value outside reasonable range\n"); |
347 |
< |
painCave.severity = OOPSE_ERROR; |
348 |
< |
painCave.isFatal = 1; |
349 |
< |
simError(); |
338 |
> |
for (int l = 0; l <= lMax_; l++) { |
339 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
340 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
341 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
342 |
> |
Qcount_[l]++; |
343 |
> |
} else { |
344 |
> |
sprintf( painCave.errMsg, |
345 |
> |
"q_l value outside reasonable range\n"); |
346 |
> |
painCave.severity = OOPSE_ERROR; |
347 |
> |
painCave.isFatal = 1; |
348 |
> |
simError(); |
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(RealType ql, RealType Wlhat) { |
369 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
370 |
> |
std::vector<ComplexType> What) { |
371 |
> |
|
372 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
373 |
|
|
374 |
< |
std::ofstream os(getOutputFileName().c_str()); |
282 |
< |
|
283 |
< |
if (os.is_open()) { |
374 |
> |
if (osq.is_open()) { |
375 |
|
|
376 |
< |
os << "# Bond Order Parameters\n"; |
377 |
< |
os << "# selection: (" << selectionScript_ << ")\n"; |
378 |
< |
os << "# \n"; |
379 |
< |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
380 |
< |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
376 |
> |
osq << "# Bond Order Parameters\n"; |
377 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
378 |
> |
osq << "# \n"; |
379 |
> |
for (int l = 0; l <= lMax_; l++) { |
380 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
381 |
> |
} |
382 |
|
// Normalize by number of frames and write it out: |
383 |
< |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
384 |
< |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
385 |
< |
os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
383 |
> |
for (int i = 0; i < nBins_; ++i) { |
384 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
385 |
> |
osq << Qval; |
386 |
> |
for (int l = 0; l <= lMax_; l++) { |
387 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
388 |
> |
} |
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 |
|
} |