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_ = 3.0; |
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); |
101 |
+ |
} |
102 |
+ |
|
103 |
|
void BondOrderParameter::process() { |
104 |
|
Molecule* mol; |
105 |
|
Atom* atom; |
114 |
|
RealType phi; |
115 |
|
RealType r; |
116 |
|
RealType dist; |
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 |
< |
|
135 |
< |
nBonds = 0; |
136 |
< |
|
137 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
138 |
< |
QBar_lm[m] = 0.0; |
139 |
< |
} |
140 |
< |
|
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(); |
165 |
+ |
nBonds = 0; |
166 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++) { |
167 |
+ |
q_lm[m] = 0.0; |
168 |
+ |
} |
169 |
|
|
170 |
|
// inner loop is over all other atoms in the system: |
171 |
|
|
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 |
< |
} |
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 |
> |
Nbonds += nBonds; |
212 |
> |
for (int m=-lNumber_; m<=lNumber_; m++) { |
213 |
> |
QBar_lm[m] += q_lm[m]; |
214 |
> |
} |
215 |
> |
} |
216 |
|
} |
217 |
|
|
218 |
|
// Normalize Qbar2 |
219 |
|
for (int m = -lNumber_;m <= lNumber_; m++){ |
220 |
< |
QBar_lm[m] /= nBonds; |
220 |
> |
QBar_lm[m] /= Nbonds; |
221 |
|
} |
222 |
|
|
223 |
|
// Find second order invariant Q_l |
257 |
|
writeOrderParameter(Q_l, real(W_l_hat)); |
258 |
|
} |
259 |
|
|
260 |
+ |
void BondOrderParameter::collectHistogram(RealType q_l) { |
261 |
|
|
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; |
268 |
+ |
} else { |
269 |
+ |
sprintf( painCave.errMsg, |
270 |
+ |
"q_l value outside reasonable range\n"); |
271 |
+ |
painCave.severity = OOPSE_ERROR; |
272 |
+ |
painCave.isFatal = 1; |
273 |
+ |
simError(); |
274 |
+ |
} |
275 |
+ |
|
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
|
279 |
|
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
280 |
|
|
281 |
|
std::ofstream os(getOutputFileName().c_str()); |
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 |
+ |
os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
294 |
+ |
} |
295 |
+ |
|
296 |
|
os.close(); |
297 |
|
|
298 |
|
} else { |