| 45 |
|
* Phys Rev B, 28,784,1983 |
| 46 |
|
* |
| 47 |
|
*/ |
| 48 |
< |
|
| 48 |
> |
|
| 49 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
| 50 |
|
#include "utils/simError.h" |
| 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 |
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|
| 58 |
+ |
BondOrderParameter::BondOrderParameter(SimInfo* info, |
| 59 |
+ |
const std::string& filename, |
| 60 |
+ |
const std::string& sele, |
| 61 |
+ |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
| 62 |
+ |
|
| 63 |
+ |
setOutputName(getPrefix(filename) + ".bo"); |
| 64 |
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|
| 65 |
< |
BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
| 66 |
< |
const std::string& sele2, double rCut, int lNumber) |
| 67 |
< |
: StaticAnalyser(info, filename), |
| 61 |
< |
selectionScript1_(sele1), evaluator1_(info), |
| 62 |
< |
seleMan1_(info){ |
| 63 |
< |
|
| 64 |
< |
setOutputName(getPrefix(filename) + ".obo"); |
| 65 |
< |
|
| 66 |
< |
evaluator1_.loadScriptString(sele1); |
| 67 |
< |
evaluator2_.loadScriptString(sele2); |
| 68 |
< |
|
| 69 |
< |
if (!evaluator1_.isDynamic()) { |
| 70 |
< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 71 |
< |
}else { |
| 72 |
< |
sprintf( painCave.errMsg, |
| 73 |
< |
"--sele1 must be static selection\n"); |
| 74 |
< |
painCave.severity = OOPSE_ERROR; |
| 75 |
< |
painCave.isFatal = 1; |
| 76 |
< |
simError(); |
| 65 |
> |
evaluator_.loadScriptString(sele); |
| 66 |
> |
if (!evaluator_.isDynamic()) { |
| 67 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 68 |
|
} |
| 69 |
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|
| 70 |
< |
/* Set up cutoff radius and type of order parameter we are calcuating*/ |
| 70 |
> |
// Set up cutoff radius and order of the Legendre Polynomial: |
| 71 |
> |
|
| 72 |
|
lNumber_ = lNumber; |
| 73 |
|
rCut_ = rCut; |
| 74 |
< |
mSize_ = 2*lNumber_+1; |
| 74 |
> |
mSize_ = 2*lNumber_+1; |
| 75 |
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|
| 76 |
< |
int i; |
| 85 |
< |
int j; |
| 86 |
< |
StuntDouble* sd1; |
| 87 |
< |
StuntDouble* sd2; |
| 88 |
< |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j); |
| 89 |
< |
sd1 != NULL && sd2 != NULL; |
| 90 |
< |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
| 91 |
< |
for (sd2 = seleMan1_.beginSelected(j),sd2 |
| 92 |
< |
sdPairs_.push_back(std::make_pair(sd1, sd2)); |
| 93 |
< |
} |
| 76 |
> |
// Q can take values from 0 to 1 |
| 77 |
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|
| 78 |
+ |
MinQ_ = 0.0; |
| 79 |
+ |
MaxQ_ = 3.0; |
| 80 |
+ |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
| 81 |
+ |
Q_histogram_.resize(nbins); |
| 82 |
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|
| 83 |
< |
} |
| 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 |
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|
| 86 |
< |
void BondOrderParameter::process |
| 87 |
< |
() { |
| 88 |
< |
Molecule* mol; |
| 89 |
< |
RigidBody* rb; |
| 102 |
< |
SimInfo::MoleculeIterator mi; |
| 103 |
< |
Molecule::RigidBodyIterator rbIter; |
| 104 |
< |
RealType theta; |
| 105 |
< |
RealType phi; |
| 106 |
< |
RealType r; |
| 107 |
< |
RealType dist; |
| 108 |
< |
RealType* QBar_lm; |
| 109 |
< |
RealType QSq_l; |
| 110 |
< |
int nBonds; |
| 111 |
< |
int m, m_index; |
| 112 |
< |
RealSphericalHarmonic sphericalHarmonic; |
| 86 |
> |
MinW_ = -0.18; |
| 87 |
> |
MaxW_ = 0.18; |
| 88 |
> |
deltaW_ = (MaxW_ - MinW_) / nbins; |
| 89 |
> |
W_histogram_.resize(nbins); |
| 90 |
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|
| 91 |
+ |
} |
| 92 |
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|
| 93 |
< |
DumpReader reader(info_, dumpFilename_); |
| 94 |
< |
int nFrames = reader.getNFrames(); |
| 93 |
> |
BondOrderParameter::~BondOrderParameter() { |
| 94 |
> |
Q_histogram_.clear(); |
| 95 |
> |
W_histogram_.clear(); |
| 96 |
> |
} |
| 97 |
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|
| 98 |
< |
/*Set the l for the spherical harmonic, it doesn't change*/ |
| 99 |
< |
sphericalHarmonic.setL(lNumber_); |
| 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 |
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|
| 103 |
< |
for (int i = 0; i < nFrames; i += step_) { |
| 104 |
< |
reader.readFrame(i); |
| 105 |
< |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 106 |
< |
nBonds = 0; |
| 103 |
> |
void BondOrderParameter::process() { |
| 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; |
| 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, Nbonds; |
| 124 |
> |
SphericalHarmonic sphericalHarmonic; |
| 125 |
> |
int i, j; |
| 126 |
> |
// Make arrays for Wigner3jm |
| 127 |
> |
double* THRCOF = new double[mSize_]; |
| 128 |
> |
// Variables for Wigner routine |
| 129 |
> |
double l_ = (double)lNumber_; |
| 130 |
> |
double m1Pass, m2Min, m2Max; |
| 131 |
> |
int error, m1, m2, m3; |
| 132 |
|
|
| 133 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 134 |
< |
//change the positions of atoms which belong to the rigidbodies |
| 128 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 129 |
< |
rb->updateAtoms(); |
| 130 |
< |
} |
| 133 |
> |
// Set the l for the spherical harmonic, it doesn't change |
| 134 |
> |
sphericalHarmonic.setL(lNumber_); |
| 135 |
|
|
| 136 |
< |
} |
| 136 |
> |
DumpReader reader(info_, dumpFilename_); |
| 137 |
> |
int nFrames = reader.getNFrames(); |
| 138 |
> |
frameCounter_ = 0; |
| 139 |
|
|
| 140 |
+ |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 141 |
+ |
reader.readFrame(istep); |
| 142 |
+ |
frameCounter_++; |
| 143 |
+ |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 144 |
+ |
|
| 145 |
+ |
if (evaluator_.isDynamic()) { |
| 146 |
+ |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 147 |
+ |
} |
| 148 |
|
|
| 149 |
< |
/* Setup QBar */ |
| 136 |
< |
QBar_lm = new double[mSize_]; |
| 149 |
> |
// update the positions of atoms which belong to the rigidbodies |
| 150 |
|
|
| 151 |
< |
/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
| 152 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 153 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 154 |
< |
currentSnapshot_->wrapVector(vec); |
| 155 |
< |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
| 156 |
< |
* we choose standard spherical coordinates */ |
| 157 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 151 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 152 |
> |
mol = info_->nextMolecule(mi)) { |
| 153 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 154 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 155 |
> |
rb->updateAtoms(); |
| 156 |
> |
} |
| 157 |
> |
} |
| 158 |
> |
|
| 159 |
> |
// outer loop is over the selected StuntDoubles: |
| 160 |
|
|
| 161 |
< |
/* Check to see if neighbor is in bond cuttoff*/ |
| 162 |
< |
if (r<rCut_){ |
| 148 |
< |
theta = atan(vec.y()/vec.x()); |
| 149 |
< |
phi = acos(vec.z()/r); |
| 150 |
< |
for(int m_index = 0; m_index < mSize_; m_index++){ |
| 151 |
< |
sphericalHarmonic.setM(m_index-lNumber_); |
| 152 |
< |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
| 153 |
< |
} |
| 154 |
< |
nBonds++; |
| 155 |
< |
} |
| 156 |
< |
} |
| 161 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 162 |
> |
sd = seleMan_.nextSelected(i)) { |
| 163 |
|
|
| 164 |
< |
/*Normalize Qbar by number of Bonds*/ |
| 165 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 166 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nBonds; |
| 167 |
< |
} |
| 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 |
> |
|
| 172 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 173 |
> |
mol = info_->nextMolecule(mi)) { |
| 174 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 175 |
> |
atom = mol->nextAtom(ai)) { |
| 176 |
|
|
| 177 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
| 178 |
|
|
| 179 |
< |
} |
| 179 |
> |
vec = sd->getPos() - atom->getPos(); |
| 180 |
> |
currentSnapshot_->wrapVector(vec); |
| 181 |
> |
|
| 182 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 183 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 184 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 185 |
> |
// system, we choose standard spherical coordinates |
| 186 |
> |
|
| 187 |
> |
r = vec.length(); |
| 188 |
> |
|
| 189 |
> |
// Check to see if neighbor is in bond cutoff |
| 190 |
> |
|
| 191 |
> |
if (r < rCut_) { |
| 192 |
> |
costheta = vec.z() / r; |
| 193 |
> |
phi = atan2(vec.y(), vec.x()); |
| 194 |
> |
|
| 195 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 196 |
> |
sphericalHarmonic.setM(m); |
| 197 |
> |
q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 198 |
> |
} |
| 199 |
> |
nBonds++; |
| 200 |
> |
} |
| 201 |
> |
} |
| 202 |
> |
} |
| 203 |
> |
} |
| 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 |
< |
/*Normalize by number of frames*/ |
| 212 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 213 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
| 211 |
> |
Nbonds += nBonds; |
| 212 |
> |
for (int m=-lNumber_; m<=lNumber_; m++) { |
| 213 |
> |
QBar_lm[m] += q_lm[m]; |
| 214 |
> |
} |
| 215 |
|
} |
| 216 |
+ |
} |
| 217 |
|
|
| 218 |
< |
|
| 219 |
< |
|
| 220 |
< |
/* Find second order invariant Q_l*/ |
| 221 |
< |
|
| 222 |
< |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
| 223 |
< |
QSq_l += pow(QBar_lm(m),2); |
| 218 |
> |
// Normalize Qbar2 |
| 219 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 220 |
> |
QBar_lm[m] /= Nbonds; |
| 221 |
> |
} |
| 222 |
> |
|
| 223 |
> |
// Find second order invariant Q_l |
| 224 |
> |
|
| 225 |
> |
QSq_l = 0.0; |
| 226 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 227 |
> |
QSq_l += norm(QBar_lm[m]); |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
std::cout << "qsl = " << QSq_l << "\n"; |
| 231 |
> |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
| 232 |
> |
|
| 233 |
> |
// Find Third Order Invariant W_l |
| 234 |
> |
|
| 235 |
> |
W_l = 0.0; |
| 236 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 237 |
> |
// Zero work array |
| 238 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
| 239 |
> |
THRCOF[ii] = 0.0; |
| 240 |
|
} |
| 241 |
< |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
| 242 |
< |
|
| 243 |
< |
/* Find Third Order Invariant W_l*/ |
| 244 |
< |
|
| 245 |
< |
/* Make arrays for Wigner3jm */ |
| 246 |
< |
double* THRCOF = new double[mSize_]; |
| 247 |
< |
/* Variables for Wigner routine */ |
| 248 |
< |
double l_ = (double)lNumber_; |
| 249 |
< |
double m2Min; |
| 250 |
< |
double m2Max; |
| 251 |
< |
int error; |
| 189 |
< |
int m1; |
| 190 |
< |
int m2; |
| 191 |
< |
int m3; |
| 192 |
< |
|
| 193 |
< |
for (int m1 = -lNumber_;m <= lNumber_;m1++){ |
| 194 |
< |
/* Zero work array */ |
| 195 |
< |
for (i=0; i<mSize_;i++){ |
| 196 |
< |
THRCOF[i] = 0.0; |
| 197 |
< |
} |
| 198 |
< |
/* Get wigner coefficients */ |
| 199 |
< |
Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error); |
| 200 |
< |
for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){ |
| 201 |
< |
m2 = floor(m2Min) + m_index - 1; |
| 202 |
< |
m3 = -m1-m2; |
| 203 |
< |
W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_); |
| 204 |
< |
} |
| 241 |
> |
// Get Wigner coefficients |
| 242 |
> |
m1Pass = (double)m1; |
| 243 |
> |
|
| 244 |
> |
Wigner3jm(&l_, &l_, &l_, |
| 245 |
> |
&m1Pass, &m2Min, &m2Max, |
| 246 |
> |
THRCOF, &mSize_, &error); |
| 247 |
> |
|
| 248 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
| 249 |
> |
m2 = (int)floor(m2Min) + mmm; |
| 250 |
> |
m3 = -m1-m2; |
| 251 |
> |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
| 252 |
|
} |
| 253 |
+ |
} |
| 254 |
+ |
|
| 255 |
+ |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 256 |
+ |
|
| 257 |
+ |
writeOrderParameter(Q_l, real(W_l_hat)); |
| 258 |
+ |
} |
| 259 |
|
|
| 260 |
+ |
void BondOrderParameter::collectHistogram(RealType q_l) { |
| 261 |
|
|
| 262 |
< |
writeOrderParameter(); |
| 263 |
< |
|
| 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 |
|
|
| 213 |
– |
void BondOrderParameter::writeOrderParameter() { |
| 278 |
|
|
| 279 |
< |
std::ofstream os(getOutputFileName().c_str()); |
| 216 |
< |
os << "#radial distribution function\n"; |
| 217 |
< |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
| 218 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 219 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 279 |
> |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
| 280 |
|
|
| 281 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 222 |
< |
os << orderParams_[i].p2 << "\t" |
| 223 |
< |
<< orderParams_[i].director[0] << "\t" |
| 224 |
< |
<< orderParams_[i].director[1] << "\t" |
| 225 |
< |
<< orderParams_[i].director[2] << "\t" |
| 226 |
< |
<< orderParams_[i].angle << "\n"; |
| 281 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 282 |
|
|
| 283 |
+ |
if (os.is_open()) { |
| 284 |
+ |
|
| 285 |
+ |
os << "# Bond Order Parameters\n"; |
| 286 |
+ |
os << "# selection: (" << selectionScript_ << ")\n"; |
| 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 |
+ |
osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
| 294 |
|
} |
| 295 |
|
|
| 296 |
< |
} |
| 296 |
> |
os.close(); |
| 297 |
|
|
| 298 |
+ |
} else { |
| 299 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 300 |
+ |
getOutputFileName().c_str()); |
| 301 |
+ |
painCave.isFatal = 1; |
| 302 |
+ |
simError(); |
| 303 |
+ |
} |
| 304 |
|
} |
| 305 |
< |
|
| 305 |
> |
} |
