| 104 |
|
Molecule* mol; |
| 105 |
|
Atom* atom; |
| 106 |
|
RigidBody* rb; |
| 107 |
+ |
int myIndex; |
| 108 |
|
SimInfo::MoleculeIterator mi; |
| 109 |
|
Molecule::RigidBodyIterator rbIter; |
| 110 |
|
Molecule::AtomIterator ai; |
| 111 |
|
StuntDouble* sd; |
| 112 |
+ |
Vector3d vec; |
| 113 |
|
RealType costheta; |
| 114 |
|
RealType phi; |
| 115 |
|
RealType r; |
| 117 |
|
std::map<int, ComplexType> QBar_lm; |
| 118 |
|
RealType QSq_l; |
| 119 |
|
RealType Q_l; |
| 120 |
+ |
ComplexType W_l; |
| 121 |
+ |
ComplexType W_l_hat; |
| 122 |
|
int nBonds; |
| 123 |
|
SphericalHarmonic sphericalHarmonic; |
| 124 |
|
int i, j; |
| 125 |
< |
|
| 125 |
> |
// Make arrays for Wigner3jm |
| 126 |
> |
double* THRCOF = new double[mSize_]; |
| 127 |
> |
// Variables for Wigner routine |
| 128 |
> |
double l_ = (double)lNumber_; |
| 129 |
> |
double m1Pass, m2Min, m2Max; |
| 130 |
> |
int error, m1, m2, m3; |
| 131 |
> |
|
| 132 |
|
// Set the l for the spherical harmonic, it doesn't change |
| 133 |
|
sphericalHarmonic.setL(lNumber_); |
| 134 |
|
|
| 125 |
– |
|
| 135 |
|
DumpReader reader(info_, dumpFilename_); |
| 136 |
|
int nFrames = reader.getNFrames(); |
| 137 |
|
frameCounter_ = 0; |
| 160 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 161 |
|
sd = seleMan_.nextSelected(i)) { |
| 162 |
|
|
| 163 |
+ |
myIndex = sd->getGlobalIndex(); |
| 164 |
+ |
|
| 165 |
|
// For this central atom, zero out nBonds and QBar_lm |
| 166 |
|
|
| 167 |
|
nBonds = 0; |
| 177 |
|
for (atom = mol->beginAtom(ai); atom != NULL; |
| 178 |
|
atom = mol->nextAtom(ai)) { |
| 179 |
|
|
| 180 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
| 181 |
|
|
| 182 |
< |
Vector3d vec = sd->getPos() - atom->getPos(); |
| 183 |
< |
currentSnapshot_->wrapVector(vec); |
| 172 |
< |
|
| 173 |
< |
// Calculate "bonds" and build Q_lm(r) where |
| 174 |
< |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 175 |
< |
// The spherical harmonics are wrt any arbitrary coordinate |
| 176 |
< |
// system, we choose standard spherical coordinates |
| 177 |
< |
|
| 178 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 179 |
< |
|
| 180 |
< |
// Check to see if neighbor is in bond cutoff |
| 181 |
< |
|
| 182 |
< |
if (r < rCut_) { |
| 183 |
< |
costheta = vec.z() / r; |
| 184 |
< |
phi = atan2(vec.y(), vec.x()); |
| 182 |
> |
vec = sd->getPos() - atom->getPos(); |
| 183 |
> |
currentSnapshot_->wrapVector(vec); |
| 184 |
|
|
| 185 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 186 |
< |
sphericalHarmonic.setM(m); |
| 187 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
| 188 |
< |
} |
| 189 |
< |
nBonds++; |
| 190 |
< |
} |
| 185 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 186 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 187 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 188 |
> |
// system, we choose standard spherical coordinates |
| 189 |
> |
|
| 190 |
> |
r = vec.length(); |
| 191 |
> |
|
| 192 |
> |
// Check to see if neighbor is in bond cutoff |
| 193 |
> |
|
| 194 |
> |
if (r < rCut_) { |
| 195 |
> |
costheta = vec.z() / r; |
| 196 |
> |
phi = atan2(vec.y(), vec.x()); |
| 197 |
> |
|
| 198 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 199 |
> |
sphericalHarmonic.setM(m); |
| 200 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
| 201 |
> |
} |
| 202 |
> |
nBonds++; |
| 203 |
> |
} |
| 204 |
> |
} |
| 205 |
|
} |
| 206 |
|
} |
| 207 |
|
|
| 208 |
|
// Normalize Qbar2 |
| 209 |
|
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 210 |
|
QBar_lm[m] /= nBonds; |
| 211 |
+ |
std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; |
| 212 |
|
} |
| 213 |
|
|
| 214 |
|
// Find second order invariant Q_l |
| 217 |
|
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 218 |
|
QSq_l += norm(QBar_lm[m]); |
| 219 |
|
} |
| 220 |
+ |
std::cout << "qsq_l = " << QSq_l << "\n"; |
| 221 |
|
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
| 207 |
– |
|
| 208 |
– |
// Find Third Order Invariant W_l |
| 222 |
|
|
| 223 |
< |
// Make arrays for Wigner3jm |
| 224 |
< |
double* THRCOF = new double[mSize_]; |
| 212 |
< |
// Variables for Wigner routine |
| 213 |
< |
double l_ = (double)lNumber_; |
| 214 |
< |
double m1Pass, m2Min, m2Max; |
| 215 |
< |
int error, m1, m2, m3; |
| 216 |
< |
|
| 217 |
< |
ComplexType W_l; |
| 218 |
< |
ComplexType W_l_hat; |
| 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 |
| 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; i < (int)(m2Max - m2Min-1.0); m_index++) { |
| 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 |
< |
|
| 240 |
> |
|
| 241 |
|
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 242 |
< |
|
| 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 |
|
|
| 248 |
|
} |
