51 |
|
#include "io/DumpReader.hpp" |
52 |
|
#include "primitives/Molecule.hpp" |
53 |
|
#include "utils/NumericConstant.hpp" |
54 |
< |
#include "math/RealSphericalHarmonic.hpp" |
54 |
> |
#include "math/SphericalHarmonic.hpp" |
55 |
> |
|
56 |
|
namespace oopse { |
57 |
|
|
57 |
– |
|
58 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
59 |
|
const std::string& filename, |
60 |
|
const std::string& sele, |
61 |
< |
double rCut, int lNumber, int nbins) |
62 |
< |
: StaticAnalyser(info, filename), selectionScript_(sele), |
63 |
< |
evaluator_(info), seleMan_(info){ |
61 |
> |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
62 |
|
|
63 |
< |
setOutputName(getPrefix(filename) + ".obo"); |
63 |
> |
setOutputName(getPrefix(filename) + ".bo"); |
64 |
|
|
65 |
|
evaluator_.loadScriptString(sele); |
66 |
|
if (!evaluator_.isDynamic()) { |
73 |
|
rCut_ = rCut; |
74 |
|
mSize_ = 2*lNumber_+1; |
75 |
|
|
76 |
< |
deltaQ_ = 1.0 / nbins; |
79 |
< |
deltaW_ = 2.0 / nbins; |
76 |
> |
// Q can take values from 0 to 1 |
77 |
|
|
78 |
+ |
MinQ_ = 0.0; |
79 |
+ |
MaxQ_ = 1.0; |
80 |
+ |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
81 |
|
Q_histogram_.resize(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_ = -0.18; |
87 |
+ |
MaxW_ = 0.18; |
88 |
+ |
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
|
W_histogram_.resize(nbins); |
90 |
|
|
91 |
|
} |
92 |
|
|
93 |
+ |
BondOrderParameter::~BondOrderParameter() { |
94 |
+ |
Q_histogram_.clear(); |
95 |
+ |
W_histogram_.clear(); |
96 |
+ |
} |
97 |
+ |
|
98 |
|
void BondOrderParameter::initalizeHistogram() { |
99 |
|
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
100 |
|
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
108 |
|
Molecule::RigidBodyIterator rbIter; |
109 |
|
Molecule::AtomIterator ai; |
110 |
|
StuntDouble* sd; |
111 |
< |
RealType theta; |
111 |
> |
RealType costheta; |
112 |
|
RealType phi; |
113 |
|
RealType r; |
114 |
|
RealType dist; |
115 |
< |
std::map<int, RealType> QBar_lm; |
115 |
> |
std::map<int, ComplexType> QBar_lm; |
116 |
|
RealType QSq_l; |
117 |
|
RealType Q_l; |
118 |
|
int nBonds; |
119 |
< |
RealSphericalHarmonic sphericalHarmonic; |
119 |
> |
SphericalHarmonic sphericalHarmonic; |
120 |
|
int i, j; |
121 |
|
|
122 |
|
// Set the l for the spherical harmonic, it doesn't change |
125 |
|
|
126 |
|
DumpReader reader(info_, dumpFilename_); |
127 |
|
int nFrames = reader.getNFrames(); |
128 |
+ |
frameCounter_ = 0; |
129 |
|
|
117 |
– |
|
130 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
131 |
|
reader.readFrame(istep); |
132 |
+ |
frameCounter_++; |
133 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
134 |
|
|
135 |
|
if (evaluator_.isDynamic()) { |
180 |
|
// Check to see if neighbor is in bond cutoff |
181 |
|
|
182 |
|
if (r < rCut_) { |
183 |
< |
theta = atan2(vec.y(), vec.x()); |
184 |
< |
phi = acos(vec.z()/r); |
183 |
> |
costheta = vec.z() / r; |
184 |
> |
phi = atan2(vec.y(), vec.x()); |
185 |
> |
|
186 |
|
for(int m = -lNumber_; m <= lNumber_; m++){ |
187 |
|
sphericalHarmonic.setM(m); |
188 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
188 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
189 |
|
} |
190 |
|
nBonds++; |
191 |
|
} |
192 |
|
} |
193 |
|
} |
194 |
|
|
195 |
< |
// Normalize Qbar |
195 |
> |
// Normalize Qbar2 |
196 |
|
for (int m = -lNumber_;m <= lNumber_; m++){ |
197 |
|
QBar_lm[m] /= nBonds; |
198 |
|
} |
201 |
|
|
202 |
|
QSq_l = 0.0; |
203 |
|
for (int m = -lNumber_; m <= lNumber_; m++){ |
204 |
< |
QSq_l += pow(QBar_lm[m], 2); |
204 |
> |
QSq_l += norm(QBar_lm[m]); |
205 |
|
} |
206 |
|
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
207 |
|
|
211 |
|
double* THRCOF = new double[mSize_]; |
212 |
|
// Variables for Wigner routine |
213 |
|
double l_ = (double)lNumber_; |
214 |
< |
double m2Min, m2Max; |
214 |
> |
double m1Pass, m2Min, m2Max; |
215 |
|
int error, m1, m2, m3; |
216 |
|
|
217 |
< |
RealType W_l; |
218 |
< |
RealType W_l_hat; |
217 |
> |
ComplexType W_l; |
218 |
> |
ComplexType W_l_hat; |
219 |
|
W_l = 0.0; |
220 |
|
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
221 |
|
// Zero work array |
223 |
|
THRCOF[i] = 0.0; |
224 |
|
} |
225 |
|
// Get Wigner coefficients |
226 |
< |
Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
226 |
> |
m1Pass = (double)m1; |
227 |
> |
Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
228 |
|
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
229 |
|
m2 = floor(m2Min) + m_index - 1; |
230 |
|
m3 = -m1-m2; |
236 |
|
|
237 |
|
// accumulate histogram data for Q_l and W_l_hat: |
238 |
|
|
239 |
< |
collectHistogram(Q_l, W_l_hat); |
239 |
> |
collectHistogram(Q_l, real(W_l_hat)); |
240 |
|
|
241 |
|
} |
242 |
|
} |
243 |
|
|
229 |
– |
// Normalize by number of frames |
230 |
– |
for (int m = -lNumber_; m <= lNumber_; m++){ |
231 |
– |
QBar_lm[m] /= nFrames; |
232 |
– |
} |
233 |
– |
|
234 |
– |
|
235 |
– |
|
236 |
– |
|
237 |
– |
|
244 |
|
writeOrderParameter(); |
245 |
|
|
246 |
|
} |
247 |
|
|
242 |
– |
|
243 |
– |
void BondOrderParameter::processHistogram() { |
244 |
– |
|
245 |
– |
int nPairs = getNPairs(); |
246 |
– |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
247 |
– |
RealType pairDensity = nPairs /volume * 2.0; |
248 |
– |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
248 |
|
|
250 |
– |
for(int i = 0 ; i < histogram_.size(); ++i){ |
251 |
– |
|
252 |
– |
RealType rLower = i * deltaR_; |
253 |
– |
RealType rUpper = rLower + deltaR_; |
254 |
– |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
255 |
– |
RealType nIdeal = volSlice * pairConstant; |
256 |
– |
|
257 |
– |
avgGofr_[i] += histogram_[i] / nIdeal; |
258 |
– |
} |
259 |
– |
|
260 |
– |
} |
261 |
– |
|
249 |
|
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
250 |
|
|
251 |
< |
if (Q_l < MaxQ_) { |
252 |
< |
int whichBin = Q_l / deltaQ_; |
253 |
< |
Q_histogram_[whichBin] += 1; |
254 |
< |
} |
255 |
< |
if (W_l_hat < MaxW_) { |
256 |
< |
int whichBin = W_l_hat / deltaW_; |
257 |
< |
W_histogram_[whichBin] += 1; |
251 |
> |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
252 |
> |
int qbin = (Q_l - MinQ_) / deltaQ_; |
253 |
> |
Q_histogram_[qbin] += 1; |
254 |
> |
Qcount_++; |
255 |
> |
sumQ_ += Q_l; |
256 |
> |
sumQ2_ += Q_l * Q_l; |
257 |
> |
} else { |
258 |
> |
sprintf( painCave.errMsg, |
259 |
> |
"Q_l value outside reasonable range\n"); |
260 |
> |
painCave.severity = OOPSE_ERROR; |
261 |
> |
painCave.isFatal = 1; |
262 |
> |
simError(); |
263 |
|
} |
272 |
– |
} |
273 |
– |
|
264 |
|
|
265 |
+ |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
266 |
+ |
int wbin = (W_l_hat - MinW_) / deltaW_; |
267 |
+ |
W_histogram_[wbin] += 1; |
268 |
+ |
Wcount_++; |
269 |
+ |
sumW_ += W_l_hat; |
270 |
+ |
sumW2_ += W_l_hat*W_l_hat; |
271 |
+ |
} else { |
272 |
+ |
sprintf( painCave.errMsg, |
273 |
+ |
"W_l_hat value outside reasonable range\n"); |
274 |
+ |
painCave.severity = OOPSE_ERROR; |
275 |
+ |
painCave.isFatal = 1; |
276 |
+ |
simError(); |
277 |
+ |
} |
278 |
+ |
} |
279 |
+ |
|
280 |
|
void BondOrderParameter::writeOrderParameter() { |
281 |
|
|
282 |
< |
std::ofstream os(getOutputFileName().c_str()); |
278 |
< |
os << "#Bond Order Parameter\n"; |
279 |
< |
os << "#selection: (" << selectionScript_ << ")\n"; |
282 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
283 |
|
|
284 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
282 |
< |
os << orderParams_[i].p2 << "\t" |
283 |
< |
<< orderParams_[i].director[0] << "\t" |
284 |
< |
<< orderParams_[i].director[1] << "\t" |
285 |
< |
<< orderParams_[i].director[2] << "\t" |
286 |
< |
<< orderParams_[i].angle << "\n"; |
284 |
> |
if (osq.is_open()) { |
285 |
|
|
286 |
+ |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
287 |
+ |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
288 |
+ |
|
289 |
+ |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
290 |
+ |
osq << "# selection: (" << selectionScript_ << ")\n"; |
291 |
+ |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
292 |
+ |
osq << "# std. dev.: " << qStdDev << "\n"; |
293 |
+ |
|
294 |
+ |
// Normalize by number of frames and write it out: |
295 |
+ |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
296 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
297 |
+ |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
298 |
+ |
} |
299 |
+ |
|
300 |
+ |
osq.close(); |
301 |
+ |
} else { |
302 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
303 |
+ |
(getOutputFileName() + "q").c_str()); |
304 |
+ |
painCave.isFatal = 1; |
305 |
+ |
simError(); |
306 |
|
} |
289 |
– |
} |
307 |
|
|
308 |
+ |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
309 |
|
|
310 |
+ |
if (osw.is_open()) { |
311 |
|
|
312 |
+ |
RealType wAvg = sumW_ / (RealType) Wcount_; |
313 |
+ |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
314 |
+ |
|
315 |
+ |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
316 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
317 |
+ |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
318 |
+ |
osw << "# std. dev.: " << wStdDev << "\n"; |
319 |
+ |
|
320 |
+ |
// Normalize by number of frames and write it out: |
321 |
+ |
for (int i = 0; i < W_histogram_.size(); ++i) { |
322 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
323 |
+ |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
osw.close(); |
327 |
+ |
} else { |
328 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
329 |
+ |
(getOutputFileName() + "w").c_str()); |
330 |
+ |
painCave.isFatal = 1; |
331 |
+ |
simError(); |
332 |
+ |
} |
333 |
+ |
} |
334 |
|
} |