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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: |
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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, 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 1.22 2006-12-20 21:03:11 gezelter 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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|
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namespace oopse { |
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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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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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|
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setOutputName(getPrefix(filename) + ".bo"); |
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|
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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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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|
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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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m2Max.clear(); |
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} |
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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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|
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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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} |
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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; |
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q[std::make_pair(l,m)] /= (RealType)nBonds; |
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|
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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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|
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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); |
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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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writeOrderParameter(Q, W_hat); |
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|
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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_; |
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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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sprintf( painCave.errMsg, |
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"q_l value outside reasonable range\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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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_); |
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W_histogram_[std::make_pair(wbin,l)] += 1; |
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Wcount_[l]++; |
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} else { |
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sprintf( painCave.errMsg, |
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"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
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painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
