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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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|
* documentation and/or other materials provided with the |
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* distribution. |
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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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* |
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* BondOrderParameter.cpp |
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* OOPSE-4 |
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* |
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> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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> |
* research, please cite the appropriate papers when you publish your |
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> |
* work. Good starting points are: |
| 35 |
> |
* |
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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, 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: BOPofR.cpp,v 1.3 2007-12-06 19:52:11 chuckv Exp $ |
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* @version $Id$ |
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* |
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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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#include "brains/Thermo.hpp" |
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|
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using namespace MATPACK; |
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namespace OpenMD { |
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|
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namespace oopse { |
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|
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BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut, |
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int nbins, RealType len) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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|
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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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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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|
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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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|
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std::pair<int,int> lm = std::make_pair(l, m1); |
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|
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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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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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|
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|
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void BOPofR::initalizeHistogram() { |
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> |
void BOPofR::initializeHistogram() { |
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for (int i = 0; i < nBins_; i++){ |
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RCount_[i] = 0; |
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WofR_[i] = 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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Vector3d rCOM; |
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RealType distCOM; |
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Vector3d pos; |
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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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std::vector<ComplexType> W; |
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std::vector<ComplexType> W_hat; |
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int nBonds, Nbonds; |
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int nBonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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|
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> |
int i; |
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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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Thermo thermo(info_); |
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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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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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W_hat.resize(lMax_+1); |
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Nbonds = 0; |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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CenterOfMass = info_->getCom(); |
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> |
CenterOfMass = thermo.getCom(); |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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} |
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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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|
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collectHistogram(q_l, w_hat, distCOM); |
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|
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if ( distCOM < len_){ |
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// Figure out where this distance goes... |
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int whichBin = distCOM / deltaR_; |
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> |
int whichBin = int(distCOM / deltaR_); |
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RCount_[whichBin]++; |
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|
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if(real(what[6]) < -0.15){ |
