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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
41 |
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* BondOrderParameter.cpp |
42 |
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* OOPSE-4 |
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* |
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* Created by J. Daniel Gezelter on 09/26/06. |
45 |
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* @author J. Daniel Gezelter |
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* @version $Id: BondOrderParameter.cpp,v 1.20 2006-11-03 22:02:55 gezelter Exp $ |
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* |
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*/ |
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|
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|
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/* Creates orientational bond order parameters as outlined by |
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
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* Phys Rev B, 28,784,1983 |
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* |
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*/ |
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|
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#include "applications/staticProps/BondOrderParameter.hpp" |
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#include "utils/simError.h" |
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele, |
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< |
double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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> |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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|
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setOutputName(getPrefix(filename) + ".bo"); |
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|
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|
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// Set up cutoff radius and order of the Legendre Polynomial: |
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|
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lMax_ = lMax; |
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rCut_ = rCut; |
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nBins_ = nbins; |
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Qcount_.resize(lMax_+1); |
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
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|
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< |
MinW_ = -0.18; |
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< |
MaxW_ = 0.18; |
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> |
MinW_ = -0.25; |
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> |
MaxW_ = 0.25; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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} |
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|
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// Make arrays for Wigner3jm |
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double* THRCOF = new double[2*lMax_+1]; |
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// Variables for Wigner routine |
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double lPass, m1Pass, m2m, m2M; |
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int error, mSize; |
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mSize = 2*lMax_+1; |
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|
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for (int l = 0; l <= lMax_; l++) { |
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lPass = (double)l; |
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for (int m1 = -l; m1 <= l; m1++) { |
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m1Pass = (double)m1; |
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|
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std::pair<int,int> lm = std::make_pair(l, m1); |
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|
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// Zero work array |
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for (int ii = 0; ii < 2*l + 1; ii++){ |
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THRCOF[ii] = 0.0; |
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} |
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|
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// Get Wigner coefficients |
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Wigner3jm(&lPass, &lPass, &lPass, |
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&m1Pass, &m2m, &m2M, |
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THRCOF, &mSize, &error); |
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|
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m2Min[lm] = (int)floor(m2m); |
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m2Max[lm] = (int)floor(m2M); |
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|
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for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
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w3j[lm].push_back(THRCOF[mmm]); |
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} |
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} |
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} |
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delete [] THRCOF; |
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THRCOF = NULL; |
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} |
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|
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BondOrderParameter::~BondOrderParameter() { |
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Q_histogram_.clear(); |
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W_histogram_.clear(); |
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+ |
for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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w3j[std::make_pair(l,m)].clear(); |
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} |
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} |
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w3j.clear(); |
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m2Min.clear(); |
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m2Max.clear(); |
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} |
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< |
|
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> |
|
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void BondOrderParameter::initalizeHistogram() { |
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for (int bin = 0; bin < nBins_; bin++) { |
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for (int l = 0; l <= lMax_; l++) { |
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RealType dist; |
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std::map<std::pair<int,int>,ComplexType> q; |
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std::vector<RealType> q_l; |
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std::vector<RealType> q2; |
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std::vector<ComplexType> w; |
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std::vector<ComplexType> w_hat; |
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std::map<std::pair<int,int>,ComplexType> QBar; |
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std::vector<RealType> Q2; |
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std::vector<RealType> Q; |
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int nBonds, Nbonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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// Make arrays for Wigner3jm |
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double* THRCOF = new double[2*lMax_+1]; |
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// Variables for Wigner routine |
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double lPass, m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3, mSize; |
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mSize = 2*lMax_+1; |
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|
|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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|
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q_l.resize(lMax_+1); |
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+ |
q2.resize(lMax_+1); |
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w.resize(lMax_+1); |
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w_hat.resize(lMax_+1); |
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|
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Q2.resize(lMax_+1); |
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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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if (atom->getGlobalIndex() != myIndex) { |
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|
|
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vec = sd->getPos() - atom->getPos(); |
233 |
< |
currentSnapshot_->wrapVector(vec); |
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> |
|
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
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q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
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|
} |
272 |
< |
collectHistogram(q_l); |
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> |
|
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> |
// Find second order invariant Q_l |
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|
|
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+ |
for (int l = 0; l <= lMax_; l++) { |
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+ |
q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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q2[l] += norm(q[std::make_pair(l,m)]); |
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} |
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q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
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(RealType)(2*l + 1))/(RealType)nBonds; |
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} |
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|
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// Find Third Order Invariant W_l |
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|
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for (int l = 0; l <= lMax_; l++) { |
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w[l] = 0.0; |
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for (int m1 = -l; m1 <= l; m1++) { |
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std::pair<int,int> lm = std::make_pair(l, m1); |
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for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
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int m2 = m2Min[lm] + mmm; |
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int m3 = -m1-m2; |
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+ |
w[l] += w3j[lm][mmm] * q[lm] * |
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q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
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} |
296 |
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} |
297 |
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|
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w_hat[l] = w[l] / pow(q2[l], 1.5); |
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} |
300 |
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|
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collectHistogram(q_l, w_hat); |
302 |
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|
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Nbonds += nBonds; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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|
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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|
} |
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|
|
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– |
|
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– |
|
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|
// Find Third Order Invariant W_l |
330 |
|
|
331 |
|
for (int l = 0; l <= lMax_; l++) { |
332 |
|
W[l] = 0.0; |
260 |
– |
lPass = (double)l; |
333 |
|
for (int m1 = -l; m1 <= l; m1++) { |
334 |
< |
// Zero work array |
335 |
< |
for (int ii = 0; ii < 2*l + 1; ii++){ |
336 |
< |
THRCOF[ii] = 0.0; |
334 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
335 |
> |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
336 |
> |
int m2 = m2Min[lm] + mmm; |
337 |
> |
int m3 = -m1-m2; |
338 |
> |
W[l] += w3j[lm][mmm] * QBar[lm] * |
339 |
> |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
340 |
|
} |
266 |
– |
// Get Wigner coefficients |
267 |
– |
m1Pass = (double)m1; |
268 |
– |
|
269 |
– |
Wigner3jm(&lPass, &lPass, &lPass, |
270 |
– |
&m1Pass, &m2Min, &m2Max, |
271 |
– |
THRCOF, &mSize, &error); |
272 |
– |
|
273 |
– |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
274 |
– |
m2 = (int)floor(m2Min) + mmm; |
275 |
– |
m3 = -m1-m2; |
276 |
– |
W[l] += THRCOF[mmm] * |
277 |
– |
QBar[std::make_pair(l,m1)] * |
278 |
– |
QBar[std::make_pair(l,m2)] * |
279 |
– |
QBar[std::make_pair(l,m3)]; |
280 |
– |
} |
341 |
|
} |
342 |
|
|
343 |
|
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
346 |
|
writeOrderParameter(Q, W_hat); |
347 |
|
} |
348 |
|
|
349 |
< |
void BondOrderParameter::collectHistogram(std::vector<RealType> q) { |
349 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
350 |
> |
std::vector<ComplexType> what) { |
351 |
|
|
352 |
|
for (int l = 0; l <= lMax_; l++) { |
353 |
|
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
363 |
|
} |
364 |
|
} |
365 |
|
|
366 |
+ |
for (int l = 0; l <= lMax_; l++) { |
367 |
+ |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
368 |
+ |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
369 |
+ |
W_histogram_[std::make_pair(wbin,l)] += 1; |
370 |
+ |
Wcount_[l]++; |
371 |
+ |
} else { |
372 |
+ |
sprintf( painCave.errMsg, |
373 |
+ |
"Re[w_hat] value outside reasonable range\n"); |
374 |
+ |
painCave.severity = OOPSE_ERROR; |
375 |
+ |
painCave.isFatal = 1; |
376 |
+ |
simError(); |
377 |
+ |
} |
378 |
+ |
} |
379 |
+ |
|
380 |
|
} |
381 |
|
|
382 |
|
|
383 |
< |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) { |
383 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
384 |
> |
std::vector<ComplexType> What) { |
385 |
|
|
386 |
< |
std::ofstream os(getOutputFileName().c_str()); |
387 |
< |
|
388 |
< |
if (os.is_open()) { |
386 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
387 |
> |
|
388 |
> |
if (osq.is_open()) { |
389 |
|
|
390 |
< |
os << "# Bond Order Parameters\n"; |
391 |
< |
os << "# selection: (" << selectionScript_ << ")\n"; |
390 |
> |
osq << "# Bond Order Parameters\n"; |
391 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
392 |
> |
osq << "# \n"; |
393 |
|
for (int l = 0; l <= lMax_; l++) { |
394 |
< |
os << "# \n"; |
318 |
< |
os << "# <Q_" << l << ">: " << Q[l] << "\n"; |
319 |
< |
os << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
394 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
395 |
|
} |
396 |
|
// Normalize by number of frames and write it out: |
397 |
|
for (int i = 0; i < nBins_; ++i) { |
398 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
399 |
< |
os << Qval; |
399 |
> |
osq << Qval; |
400 |
|
for (int l = 0; l <= lMax_; l++) { |
401 |
< |
os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
401 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]*deltaQ_/ |
402 |
> |
(RealType)Qcount_[l]; |
403 |
|
} |
404 |
< |
os << "\n"; |
404 |
> |
osq << "\n"; |
405 |
|
} |
406 |
|
|
407 |
< |
os.close(); |
407 |
> |
osq.close(); |
408 |
|
|
409 |
|
} else { |
410 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
411 |
< |
getOutputFileName().c_str()); |
411 |
> |
(getOutputFileName() + "q").c_str()); |
412 |
|
painCave.isFatal = 1; |
413 |
|
simError(); |
414 |
|
} |
415 |
+ |
|
416 |
+ |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
417 |
+ |
|
418 |
+ |
if (osw.is_open()) { |
419 |
+ |
osw << "# Bond Order Parameters\n"; |
420 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
421 |
+ |
osw << "# \n"; |
422 |
+ |
for (int l = 0; l <= lMax_; l++) { |
423 |
+ |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
424 |
+ |
} |
425 |
+ |
// Normalize by number of frames and write it out: |
426 |
+ |
for (int i = 0; i < nBins_; ++i) { |
427 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
428 |
+ |
osw << Wval; |
429 |
+ |
for (int l = 0; l <= lMax_; l++) { |
430 |
+ |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]*deltaW_/ |
431 |
+ |
(RealType)Wcount_[l]; |
432 |
+ |
} |
433 |
+ |
osw << "\n"; |
434 |
+ |
} |
435 |
+ |
|
436 |
+ |
osw.close(); |
437 |
+ |
} else { |
438 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
439 |
+ |
(getOutputFileName() + "w").c_str()); |
440 |
+ |
painCave.isFatal = 1; |
441 |
+ |
simError(); |
442 |
+ |
} |
443 |
+ |
|
444 |
|
} |
445 |
|
} |