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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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< |
* |
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> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by J. Daniel Gezelter on 09/26/06. |
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* @author J. Daniel Gezelter |
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* @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $ |
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* @version $Id$ |
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* |
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*/ |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/Wigner3jm.hpp" |
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using namespace MATPACK; |
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namespace OpenMD { |
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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 nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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double rCut, int nbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), seleMan_(info), |
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evaluator_(info) { |
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setOutputName(getPrefix(filename) + ".bo"); |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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// Make arrays for Wigner3jm |
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double* THRCOF = new double[2*lMax_+1]; |
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RealType* THRCOF = new RealType[2*lMax_+1]; |
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// Variables for Wigner routine |
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double lPass, m1Pass, m2m, m2M; |
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RealType lPass, m1Pass, m2m, m2M; |
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int error, mSize; |
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mSize = 2*lMax_+1; |
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for (int l = 0; l <= lMax_; l++) { |
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lPass = (double)l; |
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lPass = (RealType)l; |
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for (int m1 = -l; m1 <= l; m1++) { |
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m1Pass = (double)m1; |
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m1Pass = (RealType)m1; |
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std::pair<int,int> lm = std::make_pair(l, m1); |
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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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Wigner3jm(lPass, lPass, lPass, |
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m1Pass, m2m, m2M, |
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THRCOF, mSize, error); |
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m2Min[lm] = (int)floor(m2m); |
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m2Max[lm] = (int)floor(m2M); |
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m2Max.clear(); |
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} |
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void BondOrderParameter::initalizeHistogram() { |
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void BondOrderParameter::initializeHistogram() { |
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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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Q_histogram_[std::make_pair(bin,l)] = 0; |
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RealType costheta; |
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RealType phi; |
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RealType r; |
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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_hat; |
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int nBonds, Nbonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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int i; |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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for(int m = -l; m <= l; m++){ |
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sphericalHarmonic.setM(m); |
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q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
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} |
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} |
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nBonds++; |
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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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q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 269 |
> |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 270 |
> |
|
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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 / (RealType)(2*l + 1)); |
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} |
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} |
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w_hat[l] = w[l] / pow(q2[l], 1.5); |
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w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
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} |
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collectHistogram(q_l, w_hat); |
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} |
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} |
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< |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
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> |
W_hat[l] = W[l] / pow(Q2[l], RealType(1.5)); |
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} |
| 337 |
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writeOrderParameter(Q, W_hat); |
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for (int l = 0; l <= lMax_; l++) { |
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if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
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< |
int qbin = (q[l] - MinQ_) / deltaQ_; |
| 346 |
> |
int qbin = int((q[l] - MinQ_) / deltaQ_); |
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Q_histogram_[std::make_pair(qbin,l)] += 1; |
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Qcount_[l]++; |
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} else { |
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for (int l = 0; l <= lMax_; l++) { |
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if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
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< |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
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> |
int wbin = int((real(what[l]) - MinW_) / deltaW_); |
| 361 |
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W_histogram_[std::make_pair(wbin,l)] += 1; |
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Wcount_[l]++; |
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} else { |
