51 |
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#include "io/DumpReader.hpp" |
52 |
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#include "primitives/Molecule.hpp" |
53 |
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#include "utils/NumericConstant.hpp" |
54 |
– |
#include "math/SphericalHarmonic.hpp" |
54 |
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|
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 |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
– |
W_histogram_.resize(nbins); |
88 |
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|
89 |
< |
} |
89 |
> |
// Make arrays for Wigner3jm |
90 |
> |
double* THRCOF = new double[2*lMax_+1]; |
91 |
> |
// Variables for Wigner routine |
92 |
> |
double lPass, m1Pass, m2m, m2M; |
93 |
> |
int error, mSize; |
94 |
> |
mSize = 2*lMax_+1; |
95 |
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|
96 |
+ |
for (int l = 0; l <= lMax_; l++) { |
97 |
+ |
lPass = (double)l; |
98 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
99 |
+ |
m1Pass = (double)m1; |
100 |
+ |
|
101 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
102 |
+ |
|
103 |
+ |
// Zero work array |
104 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
105 |
+ |
THRCOF[ii] = 0.0; |
106 |
+ |
} |
107 |
+ |
|
108 |
+ |
// Get Wigner coefficients |
109 |
+ |
Wigner3jm(&lPass, &lPass, &lPass, |
110 |
+ |
&m1Pass, &m2m, &m2M, |
111 |
+ |
THRCOF, &mSize, &error); |
112 |
+ |
|
113 |
+ |
m2Min[lm] = (int)floor(m2m); |
114 |
+ |
m2Max[lm] = (int)floor(m2M); |
115 |
+ |
|
116 |
+ |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
117 |
+ |
w3j[lm].push_back(THRCOF[mmm]); |
118 |
+ |
} |
119 |
+ |
} |
120 |
+ |
} |
121 |
+ |
} |
122 |
+ |
|
123 |
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BondOrderParameter::~BondOrderParameter() { |
124 |
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Q_histogram_.clear(); |
125 |
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W_histogram_.clear(); |
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} |
127 |
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|
128 |
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void BondOrderParameter::initalizeHistogram() { |
129 |
< |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
130 |
< |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
129 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
130 |
> |
for (int l = 0; l <= lMax_; l++) { |
131 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
132 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
133 |
> |
} |
134 |
> |
} |
135 |
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} |
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|
137 |
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void BondOrderParameter::process() { |
148 |
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RealType phi; |
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RealType r; |
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RealType dist; |
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< |
std::map<int,ComplexType> QBar_lm; |
152 |
< |
RealType QSq_l; |
153 |
< |
RealType Q_l; |
154 |
< |
ComplexType W_l; |
155 |
< |
ComplexType W_l_hat; |
156 |
< |
int nBonds; |
151 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
152 |
> |
std::vector<RealType> q_l; |
153 |
> |
std::vector<RealType> q2; |
154 |
> |
std::vector<ComplexType> w; |
155 |
> |
std::vector<ComplexType> w_hat; |
156 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
157 |
> |
std::vector<RealType> Q2; |
158 |
> |
std::vector<RealType> Q; |
159 |
> |
std::vector<ComplexType> W; |
160 |
> |
std::vector<ComplexType> W_hat; |
161 |
> |
int nBonds, Nbonds; |
162 |
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SphericalHarmonic sphericalHarmonic; |
163 |
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int i, j; |
125 |
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// Make arrays for Wigner3jm |
126 |
– |
double* THRCOF = new double[mSize_]; |
127 |
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// Variables for Wigner routine |
128 |
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double l_ = (double)lNumber_; |
129 |
– |
double m1Pass, m2Min, m2Max; |
130 |
– |
int error, m1, m2, m3; |
164 |
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|
132 |
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// Set the l for the spherical harmonic, it doesn't change |
133 |
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sphericalHarmonic.setL(lNumber_); |
134 |
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|
165 |
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DumpReader reader(info_, dumpFilename_); |
166 |
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int nFrames = reader.getNFrames(); |
167 |
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frameCounter_ = 0; |
168 |
+ |
|
169 |
+ |
q_l.resize(lMax_+1); |
170 |
+ |
q2.resize(lMax_+1); |
171 |
+ |
w.resize(lMax_+1); |
172 |
+ |
w_hat.resize(lMax_+1); |
173 |
+ |
|
174 |
+ |
Q2.resize(lMax_+1); |
175 |
+ |
Q.resize(lMax_+1); |
176 |
+ |
W.resize(lMax_+1); |
177 |
+ |
W_hat.resize(lMax_+1); |
178 |
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|
179 |
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for (int istep = 0; istep < nFrames; istep += step_) { |
180 |
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reader.readFrame(istep); |
193 |
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rb = mol->nextRigidBody(rbIter)) { |
194 |
|
rb->updateAtoms(); |
195 |
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} |
196 |
< |
} |
197 |
< |
|
196 |
> |
} |
197 |
> |
|
198 |
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// outer loop is over the selected StuntDoubles: |
199 |
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|
200 |
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
201 |
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sd = seleMan_.nextSelected(i)) { |
202 |
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|
203 |
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myIndex = sd->getGlobalIndex(); |
164 |
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|
165 |
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// For this central atom, zero out nBonds and QBar_lm |
166 |
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|
204 |
|
nBonds = 0; |
205 |
< |
|
206 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
207 |
< |
QBar_lm[m] = 0.0; |
205 |
> |
|
206 |
> |
for (int l = 0; l <= lMax_; l++) { |
207 |
> |
for (int m = -l; m <= l; m++) { |
208 |
> |
q[std::make_pair(l,m)] = 0.0; |
209 |
> |
} |
210 |
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} |
211 |
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|
212 |
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// inner loop is over all other atoms in the system: |
233 |
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if (r < rCut_) { |
234 |
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costheta = vec.z() / r; |
235 |
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phi = atan2(vec.y(), vec.x()); |
236 |
< |
|
237 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
238 |
< |
sphericalHarmonic.setM(m); |
239 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
236 |
> |
|
237 |
> |
for (int l = 0; l <= lMax_; l++) { |
238 |
> |
sphericalHarmonic.setL(l); |
239 |
> |
for(int m = -l; m <= l; m++){ |
240 |
> |
sphericalHarmonic.setM(m); |
241 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
242 |
> |
} |
243 |
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} |
244 |
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nBonds++; |
245 |
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} |
247 |
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} |
248 |
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} |
249 |
|
|
250 |
< |
// Normalize Qbar2 |
251 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
252 |
< |
QBar_lm[m] /= nBonds; |
250 |
> |
|
251 |
> |
for (int l = 0; l <= lMax_; l++) { |
252 |
> |
q_l[l] = 0.0; |
253 |
> |
for(int m = -l; m <= l; m++) { |
254 |
> |
q_l[l] += norm(q[std::make_pair(l,m)]); |
255 |
> |
} |
256 |
> |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
257 |
> |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
258 |
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} |
259 |
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|
260 |
|
// Find second order invariant Q_l |
261 |
< |
|
262 |
< |
QSq_l = 0.0; |
263 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
264 |
< |
QSq_l += norm(QBar_lm[m]); |
261 |
> |
|
262 |
> |
for (int l = 0; l <= lMax_; l++) { |
263 |
> |
q2[l] = 0.0; |
264 |
> |
for (int m = -l; m <= l; m++){ |
265 |
> |
q2[l] += norm(q[std::make_pair(l,m)]); |
266 |
> |
} |
267 |
> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
268 |
> |
(RealType)(2*l + 1))/(RealType)nBonds; |
269 |
|
} |
270 |
|
|
220 |
– |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / |
221 |
– |
(2.0*(RealType)lNumber_ + 1.0)); |
222 |
– |
|
271 |
|
// Find Third Order Invariant W_l |
272 |
< |
|
273 |
< |
W_l = 0.0; |
274 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
275 |
< |
// Zero work array |
276 |
< |
for (int ii = 0; ii < mSize_; ii++){ |
277 |
< |
THRCOF[ii] = 0.0; |
272 |
> |
|
273 |
> |
for (int l = 0; l <= lMax_; l++) { |
274 |
> |
w[l] = 0.0; |
275 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
276 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
277 |
> |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
278 |
> |
int m2 = m2Min[lm] + mmm; |
279 |
> |
int m3 = -m1-m2; |
280 |
> |
w[l] += w3j[lm][mmm] * q[lm] * |
281 |
> |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
282 |
> |
} |
283 |
|
} |
284 |
< |
// Get Wigner coefficients |
285 |
< |
m1Pass = (double)m1; |
284 |
> |
|
285 |
> |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
286 |
> |
} |
287 |
|
|
288 |
< |
Wigner3jm(&l_, &l_, &l_, |
289 |
< |
&m1Pass, &m2Min, &m2Max, |
290 |
< |
THRCOF, &mSize_, &error); |
291 |
< |
|
292 |
< |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
293 |
< |
m2 = (int)floor(m2Min) + mmm; |
240 |
< |
m3 = -m1-m2; |
241 |
< |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
288 |
> |
collectHistogram(q_l, w_hat); |
289 |
> |
|
290 |
> |
Nbonds += nBonds; |
291 |
> |
for (int l = 0; l <= lMax_; l++) { |
292 |
> |
for (int m = -l; m <= l; m++) { |
293 |
> |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
294 |
|
} |
295 |
|
} |
244 |
– |
|
245 |
– |
W_l_hat = W_l / pow(QSq_l, 1.5); |
246 |
– |
|
247 |
– |
// accumulate histogram data for Q_l and W_l_hat: |
248 |
– |
|
249 |
– |
std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; |
250 |
– |
collectHistogram(Q_l, real(W_l_hat)); |
251 |
– |
|
296 |
|
} |
297 |
|
} |
298 |
+ |
|
299 |
+ |
// Normalize Qbar2 |
300 |
+ |
for (int l = 0; l <= lMax_; l++) { |
301 |
+ |
for (int m = -l; m <= l; m++){ |
302 |
+ |
QBar[std::make_pair(l,m)] /= Nbonds; |
303 |
+ |
} |
304 |
+ |
} |
305 |
|
|
306 |
< |
writeOrderParameter(); |
306 |
> |
// Find second order invariant Q_l |
307 |
|
|
308 |
+ |
for (int l = 0; l <= lMax_; l++) { |
309 |
+ |
Q2[l] = 0.0; |
310 |
+ |
for (int m = -l; m <= l; m++){ |
311 |
+ |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
312 |
+ |
} |
313 |
+ |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
314 |
+ |
} |
315 |
+ |
|
316 |
+ |
// Find Third Order Invariant W_l |
317 |
+ |
|
318 |
+ |
for (int l = 0; l <= lMax_; l++) { |
319 |
+ |
W[l] = 0.0; |
320 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
321 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
322 |
+ |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
323 |
+ |
int m2 = m2Min[lm] + mmm; |
324 |
+ |
int m3 = -m1-m2; |
325 |
+ |
W[l] += w3j[lm][mmm] * QBar[lm] * |
326 |
+ |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
327 |
+ |
} |
328 |
+ |
} |
329 |
+ |
|
330 |
+ |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
writeOrderParameter(Q, W_hat); |
334 |
|
} |
335 |
|
|
336 |
+ |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
337 |
+ |
std::vector<ComplexType> what) { |
338 |
|
|
339 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
340 |
< |
|
341 |
< |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
342 |
< |
int qbin = (Q_l - MinQ_) / deltaQ_; |
343 |
< |
Q_histogram_[qbin] += 1; |
344 |
< |
Qcount_++; |
345 |
< |
sumQ_ += Q_l; |
346 |
< |
sumQ2_ += Q_l * Q_l; |
347 |
< |
} else { |
348 |
< |
sprintf( painCave.errMsg, |
349 |
< |
"Q_l value outside reasonable range\n"); |
350 |
< |
painCave.severity = OOPSE_ERROR; |
272 |
< |
painCave.isFatal = 1; |
273 |
< |
simError(); |
339 |
> |
for (int l = 0; l <= lMax_; l++) { |
340 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
341 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
342 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
343 |
> |
Qcount_[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(); |
350 |
> |
} |
351 |
|
} |
352 |
|
|
353 |
< |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
354 |
< |
int wbin = (W_l_hat - MinW_) / deltaW_; |
355 |
< |
W_histogram_[wbin] += 1; |
356 |
< |
Wcount_++; |
357 |
< |
sumW_ += W_l_hat; |
358 |
< |
sumW2_ += W_l_hat*W_l_hat; |
359 |
< |
} else { |
360 |
< |
sprintf( painCave.errMsg, |
361 |
< |
"W_l_hat value outside reasonable range\n"); |
362 |
< |
painCave.severity = OOPSE_ERROR; |
363 |
< |
painCave.isFatal = 1; |
364 |
< |
simError(); |
353 |
> |
for (int l = 0; l <= lMax_; l++) { |
354 |
> |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
355 |
> |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
356 |
> |
W_histogram_[std::make_pair(wbin,l)] += 1; |
357 |
> |
Wcount_[l]++; |
358 |
> |
} else { |
359 |
> |
sprintf( painCave.errMsg, |
360 |
> |
"Re[w_hat] value outside reasonable range\n"); |
361 |
> |
painCave.severity = OOPSE_ERROR; |
362 |
> |
painCave.isFatal = 1; |
363 |
> |
simError(); |
364 |
> |
} |
365 |
|
} |
366 |
+ |
|
367 |
|
} |
368 |
|
|
291 |
– |
void BondOrderParameter::writeOrderParameter() { |
369 |
|
|
370 |
+ |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
371 |
+ |
std::vector<ComplexType> What) { |
372 |
+ |
|
373 |
|
std::ofstream osq((getOutputFileName() + "q").c_str()); |
374 |
|
|
375 |
|
if (osq.is_open()) { |
296 |
– |
|
297 |
– |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
298 |
– |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
376 |
|
|
377 |
< |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
377 |
> |
osq << "# Bond Order Parameters\n"; |
378 |
|
osq << "# selection: (" << selectionScript_ << ")\n"; |
379 |
< |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
380 |
< |
osq << "# std. dev.: " << qStdDev << "\n"; |
381 |
< |
|
379 |
> |
osq << "# \n"; |
380 |
> |
for (int l = 0; l <= lMax_; l++) { |
381 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
382 |
> |
} |
383 |
|
// Normalize by number of frames and write it out: |
384 |
< |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
385 |
< |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
386 |
< |
osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
384 |
> |
for (int i = 0; i < nBins_; ++i) { |
385 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
386 |
> |
osq << Qval; |
387 |
> |
for (int l = 0; l <= lMax_; l++) { |
388 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
389 |
> |
} |
390 |
> |
osq << "\n"; |
391 |
|
} |
392 |
< |
|
392 |
> |
|
393 |
|
osq.close(); |
394 |
+ |
|
395 |
|
} else { |
396 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
397 |
|
(getOutputFileName() + "q").c_str()); |
402 |
|
std::ofstream osw((getOutputFileName() + "w").c_str()); |
403 |
|
|
404 |
|
if (osw.is_open()) { |
405 |
< |
|
323 |
< |
RealType wAvg = sumW_ / (RealType) Wcount_; |
324 |
< |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
325 |
< |
|
326 |
< |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
405 |
> |
osw << "# Bond Order Parameters\n"; |
406 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
407 |
< |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
408 |
< |
osw << "# std. dev.: " << wStdDev << "\n"; |
409 |
< |
|
407 |
> |
osw << "# \n"; |
408 |
> |
for (int l = 0; l <= lMax_; l++) { |
409 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
410 |
> |
} |
411 |
|
// Normalize by number of frames and write it out: |
412 |
< |
for (int i = 0; i < W_histogram_.size(); ++i) { |
413 |
< |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
414 |
< |
osw << Wval << "\t" << (RealType)W_histogram_[i] / (RealType)Wcount_ << "\n"; |
412 |
> |
for (int i = 0; i < nBins_; ++i) { |
413 |
> |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
414 |
> |
osw << Wval; |
415 |
> |
for (int l = 0; l <= lMax_; l++) { |
416 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l]; |
417 |
> |
} |
418 |
> |
osw << "\n"; |
419 |
|
} |
420 |
< |
|
420 |
> |
|
421 |
|
osw.close(); |
422 |
|
} else { |
423 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
425 |
|
painCave.isFatal = 1; |
426 |
|
simError(); |
427 |
|
} |
428 |
+ |
|
429 |
|
} |
430 |
|
} |