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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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* [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 1442 2010-05-10 17:28:26Z gezelter $ |
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StuntDouble* sd2; |
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StuntDouble* sdi; |
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StuntDouble* sdj; |
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StuntDouble* sdk; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Vector3d vec; |
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Vector3d ri, rj, rk, rik, rkj, dposition, tposition; |
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RealType r; |
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RealType dist; |
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RealType cospsi; |
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RealType Qk; |
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std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; |
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// Use only the 4 closest neighbors to do the rest of the work: |
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int nbors = myNeighbors.size(); |
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// > 4 ? 4 : myNeighbors.size(); |
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int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size(); |
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int nang = int (0.5 * (nbors * (nbors - 1))); |
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rk = sd->getPos(); |
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std::cerr<<nbors<<endl; |
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for (int i = 0; i < nbors-1; i++) { |
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sdi = myNeighbors[i].second; |
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// Calculates scaled Qk for each molecule using calculated angles from 4 or fewer nearest neighbors. |
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Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); |
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> |
//std::cerr<<Qk<<"\t"<<nang<<endl; |
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} |
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} |
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//std::cerr<<nang<<endl; |
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if (nang > 0) { |
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collectHistogram(Qk); |
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// Saves positions of StuntDoubles & neighbors with distorted coordination (low Qk value) |
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if ((Qk < 0.55) && (Qk > 0.45)) { |
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//std::cerr<<Distorted_.size()<<endl; |
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Distorted_.push_back(sd); |
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> |
//std::cerr<<Distorted_.size()<<endl; |
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dposition = sd->getPos(); |
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//std::cerr << "distorted position \t" << dposition << "\n"; |
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} |
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// Saves positions of StuntDoubles & neighbors with tetrahedral coordination (high Qk value) |
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if (Qk > 0.95) { |
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> |
if (Qk > 0.05) { |
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Tetrahedral_.push_back(sd); |
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tposition = sd->getPos(); |
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//std::cerr << "tetrahedral position \t" << tposition << "\n"; |
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} |
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+ |
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//std::cerr<<Tetrahedral_.size()<<endl; |
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+ |
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} |
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} |
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for (int i = 0; i < nBins_; ++i) { |
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nSelected = nSelected + Q_histogram_[i]*deltaQ_; |
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} |
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> |
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std::ofstream osq((getOutputFileName() + "Q").c_str()); |
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if (osq.is_open()) { |
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osd << "1000000.00000000; 34.52893134 0.00000000 0.00000000; 0.00000000 34.52893134 0.00000000; 0.00000000 0.00000000 34.52893134" << "\n"; |
| 304 |
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for (iter = Distorted_.begin(); iter != Distorted_.end(); ++iter) { |
| 306 |
– |
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Vector3d position; |
| 308 |
– |
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position = (*iter)->getPos(); |
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osd << "O " << "\t"; |
| 309 |
< |
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| 313 |
< |
for (int z=0; z<position.size(); z++) { |
| 314 |
< |
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> |
for (unsigned int z = 0; z < position.size(); z++) { |
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osd << position[z] << " " << "\t"; |
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} |
| 317 |
– |
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| 312 |
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osd << "\n"; |
| 319 |
– |
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| 313 |
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} |
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– |
|
| 314 |
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osd.close(); |
| 315 |
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} |
| 316 |
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| 331 |
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| 332 |
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ost << "O " << "\t"; |
| 333 |
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|
| 334 |
< |
for (int z=0; z<position.size(); z++) { |
| 334 |
> |
for (unsigned int z = 0; z < position.size(); z++) { |
| 335 |
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|
| 336 |
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ost << position[z] << " " << "\t"; |
| 337 |
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} |
