| 72 |
|
lNumber_ = lNumber; |
| 73 |
|
rCut_ = rCut; |
| 74 |
|
mSize_ = 2*lNumber_+1; |
| 75 |
– |
|
| 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 |
– |
|
| 75 |
|
} |
| 76 |
|
|
| 77 |
|
BondOrderParameter::~BondOrderParameter() { |
| 94 |
– |
Q_histogram_.clear(); |
| 95 |
– |
W_histogram_.clear(); |
| 78 |
|
} |
| 79 |
|
|
| 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 |
– |
|
| 80 |
|
void BondOrderParameter::process() { |
| 81 |
|
Molecule* mol; |
| 82 |
|
Atom* atom; |
| 83 |
|
RigidBody* rb; |
| 84 |
+ |
int myIndex; |
| 85 |
|
SimInfo::MoleculeIterator mi; |
| 86 |
|
Molecule::RigidBodyIterator rbIter; |
| 87 |
|
Molecule::AtomIterator ai; |
| 88 |
|
StuntDouble* sd; |
| 89 |
+ |
Vector3d vec; |
| 90 |
|
RealType costheta; |
| 91 |
|
RealType phi; |
| 92 |
|
RealType r; |
| 93 |
|
RealType dist; |
| 94 |
< |
std::map<int, ComplexType> QBar_lm; |
| 94 |
> |
std::map<int,ComplexType> QBar_lm; |
| 95 |
|
RealType QSq_l; |
| 96 |
|
RealType Q_l; |
| 97 |
+ |
ComplexType W_l; |
| 98 |
+ |
ComplexType W_l_hat; |
| 99 |
|
int nBonds; |
| 100 |
|
SphericalHarmonic sphericalHarmonic; |
| 101 |
|
int i, j; |
| 102 |
< |
|
| 102 |
> |
// Make arrays for Wigner3jm |
| 103 |
> |
double* THRCOF = new double[mSize_]; |
| 104 |
> |
// Variables for Wigner routine |
| 105 |
> |
double l_ = (double)lNumber_; |
| 106 |
> |
double m1Pass, m2Min, m2Max; |
| 107 |
> |
int error, m1, m2, m3; |
| 108 |
> |
|
| 109 |
|
// Set the l for the spherical harmonic, it doesn't change |
| 110 |
|
sphericalHarmonic.setL(lNumber_); |
| 111 |
|
|
| 125 |
– |
|
| 112 |
|
DumpReader reader(info_, dumpFilename_); |
| 113 |
|
int nFrames = reader.getNFrames(); |
| 114 |
|
frameCounter_ = 0; |
| 132 |
|
} |
| 133 |
|
} |
| 134 |
|
|
| 135 |
+ |
nBonds = 0; |
| 136 |
+ |
|
| 137 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 138 |
+ |
QBar_lm[m] = 0.0; |
| 139 |
+ |
} |
| 140 |
+ |
|
| 141 |
|
// outer loop is over the selected StuntDoubles: |
| 142 |
|
|
| 143 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 144 |
|
sd = seleMan_.nextSelected(i)) { |
| 145 |
|
|
| 146 |
< |
// For this central atom, zero out nBonds and QBar_lm |
| 155 |
< |
|
| 156 |
< |
nBonds = 0; |
| 157 |
< |
|
| 158 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 159 |
< |
QBar_lm[m] = 0.0; |
| 160 |
< |
} |
| 146 |
> |
myIndex = sd->getGlobalIndex(); |
| 147 |
|
|
| 148 |
|
// inner loop is over all other atoms in the system: |
| 149 |
|
|
| 152 |
|
for (atom = mol->beginAtom(ai); atom != NULL; |
| 153 |
|
atom = mol->nextAtom(ai)) { |
| 154 |
|
|
| 155 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
| 156 |
|
|
| 157 |
< |
Vector3d vec = sd->getPos() - atom->getPos(); |
| 158 |
< |
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()); |
| 157 |
> |
vec = sd->getPos() - atom->getPos(); |
| 158 |
> |
currentSnapshot_->wrapVector(vec); |
| 159 |
|
|
| 160 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 161 |
< |
sphericalHarmonic.setM(m); |
| 162 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
| 163 |
< |
} |
| 164 |
< |
nBonds++; |
| 165 |
< |
} |
| 160 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 161 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 162 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 163 |
> |
// system, we choose standard spherical coordinates |
| 164 |
> |
|
| 165 |
> |
r = vec.length(); |
| 166 |
> |
|
| 167 |
> |
// Check to see if neighbor is in bond cutoff |
| 168 |
> |
|
| 169 |
> |
if (r < rCut_) { |
| 170 |
> |
costheta = vec.z() / r; |
| 171 |
> |
phi = atan2(vec.y(), vec.x()); |
| 172 |
> |
|
| 173 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 174 |
> |
sphericalHarmonic.setM(m); |
| 175 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 176 |
> |
} |
| 177 |
> |
nBonds++; |
| 178 |
> |
} |
| 179 |
> |
} |
| 180 |
|
} |
| 181 |
|
} |
| 182 |
< |
|
| 183 |
< |
// Normalize Qbar2 |
| 196 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 197 |
< |
QBar_lm[m] /= nBonds; |
| 198 |
< |
} |
| 199 |
< |
|
| 200 |
< |
// Find second order invariant Q_l |
| 201 |
< |
|
| 202 |
< |
QSq_l = 0.0; |
| 203 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 204 |
< |
QSq_l += norm(QBar_lm[m]); |
| 205 |
< |
} |
| 206 |
< |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
| 207 |
< |
|
| 208 |
< |
// Find Third Order Invariant W_l |
| 209 |
< |
|
| 210 |
< |
// Make arrays for Wigner3jm |
| 211 |
< |
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; |
| 219 |
< |
W_l = 0.0; |
| 220 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 221 |
< |
// Zero work array |
| 222 |
< |
for (int ii = 0; ii < mSize_; ii++){ |
| 223 |
< |
THRCOF[i] = 0.0; |
| 224 |
< |
} |
| 225 |
< |
// Get Wigner coefficients |
| 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; |
| 231 |
< |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
| 232 |
< |
} |
| 233 |
< |
} |
| 182 |
> |
} |
| 183 |
> |
} |
| 184 |
|
|
| 185 |
< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 186 |
< |
|
| 187 |
< |
// accumulate histogram data for Q_l and W_l_hat: |
| 238 |
< |
|
| 239 |
< |
collectHistogram(Q_l, real(W_l_hat)); |
| 240 |
< |
|
| 241 |
< |
} |
| 185 |
> |
// Normalize Qbar2 |
| 186 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 187 |
> |
QBar_lm[m] /= nBonds; |
| 188 |
|
} |
| 189 |
|
|
| 190 |
< |
writeOrderParameter(); |
| 190 |
> |
// Find second order invariant Q_l |
| 191 |
|
|
| 192 |
< |
} |
| 193 |
< |
|
| 194 |
< |
|
| 249 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
| 250 |
< |
|
| 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(); |
| 192 |
> |
QSq_l = 0.0; |
| 193 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 194 |
> |
QSq_l += norm(QBar_lm[m]); |
| 195 |
|
} |
| 196 |
< |
|
| 197 |
< |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
| 198 |
< |
int wbin = (W_l_hat - MinW_) / deltaW_; |
| 199 |
< |
W_histogram_[wbin] += 1; |
| 200 |
< |
Wcount_++; |
| 201 |
< |
sumW_ += W_l_hat; |
| 202 |
< |
sumW2_ += W_l_hat*W_l_hat; |
| 203 |
< |
} else { |
| 204 |
< |
sprintf( painCave.errMsg, |
| 205 |
< |
"W_l_hat value outside reasonable range\n"); |
| 206 |
< |
painCave.severity = OOPSE_ERROR; |
| 207 |
< |
painCave.isFatal = 1; |
| 208 |
< |
simError(); |
| 209 |
< |
} |
| 278 |
< |
} |
| 279 |
< |
|
| 280 |
< |
void BondOrderParameter::writeOrderParameter() { |
| 281 |
< |
|
| 282 |
< |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
| 283 |
< |
|
| 284 |
< |
if (osq.is_open()) { |
| 285 |
< |
|
| 286 |
< |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
| 287 |
< |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
| 196 |
> |
|
| 197 |
> |
std::cout << "qsl = " << QSq_l << "\n"; |
| 198 |
> |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
| 199 |
> |
|
| 200 |
> |
// Find Third Order Invariant W_l |
| 201 |
> |
|
| 202 |
> |
W_l = 0.0; |
| 203 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 204 |
> |
// Zero work array |
| 205 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
| 206 |
> |
THRCOF[ii] = 0.0; |
| 207 |
> |
} |
| 208 |
> |
// Get Wigner coefficients |
| 209 |
> |
m1Pass = (double)m1; |
| 210 |
|
|
| 211 |
< |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
| 212 |
< |
osq << "# selection: (" << selectionScript_ << ")\n"; |
| 213 |
< |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
| 292 |
< |
osq << "# std. dev.: " << qStdDev << "\n"; |
| 211 |
> |
Wigner3jm(&l_, &l_, &l_, |
| 212 |
> |
&m1Pass, &m2Min, &m2Max, |
| 213 |
> |
THRCOF, &mSize_, &error); |
| 214 |
|
|
| 215 |
< |
// Normalize by number of frames and write it out: |
| 216 |
< |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
| 217 |
< |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 218 |
< |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
| 215 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
| 216 |
> |
m2 = (int)floor(m2Min) + mmm; |
| 217 |
> |
m3 = -m1-m2; |
| 218 |
> |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
| 219 |
|
} |
| 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(); |
| 220 |
|
} |
| 221 |
+ |
|
| 222 |
+ |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 223 |
+ |
|
| 224 |
+ |
writeOrderParameter(Q_l, real(W_l_hat)); |
| 225 |
+ |
} |
| 226 |
|
|
| 308 |
– |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
| 227 |
|
|
| 228 |
< |
if (osw.is_open()) { |
| 228 |
> |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
| 229 |
|
|
| 230 |
< |
RealType wAvg = sumW_ / (RealType) Wcount_; |
| 231 |
< |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
| 230 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 231 |
> |
|
| 232 |
> |
if (os.is_open()) { |
| 233 |
|
|
| 234 |
< |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
| 235 |
< |
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 236 |
< |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
| 237 |
< |
osw << "# std. dev.: " << wStdDev << "\n"; |
| 238 |
< |
|
| 239 |
< |
// Normalize by number of frames and write it out: |
| 240 |
< |
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(); |
| 234 |
> |
os << "# Bond Order Parameters\n"; |
| 235 |
> |
os << "# selection: (" << selectionScript_ << ")\n"; |
| 236 |
> |
os << "# \n"; |
| 237 |
> |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
| 238 |
> |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
| 239 |
> |
os.close(); |
| 240 |
> |
|
| 241 |
|
} else { |
| 242 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 243 |
< |
(getOutputFileName() + "w").c_str()); |
| 243 |
> |
getOutputFileName().c_str()); |
| 244 |
|
painCave.isFatal = 1; |
| 245 |
|
simError(); |
| 246 |
|
} |
