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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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* |
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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 1442 2010-05-10 17:28:26Z gezelter $ |
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* |
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*/ |
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|
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#include "applications/staticProps/TetrahedralityParam.hpp" |
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#include "utils/simError.h" |
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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 <vector> |
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|
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namespace OpenMD { |
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|
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TetrahedralityParam::TetrahedralityParam(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) : |
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StaticAnalyser(info, filename), selectionScript_(sele), |
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seleMan_(info), evaluator_(info) { |
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|
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setOutputName(getPrefix(filename) + ".q"); |
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|
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evaluator_.loadScriptString(sele); |
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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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// Set up cutoff radius: |
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|
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rCut_ = rCut; |
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nBins_ = nbins; |
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|
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Q_histogram_.resize(nBins_); |
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|
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// Q can take values from 0 to 1 |
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|
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MinQ_ = 0.0; |
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MaxQ_ = 1.1; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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|
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} |
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|
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TetrahedralityParam::~TetrahedralityParam() { |
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Q_histogram_.clear(); |
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} |
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|
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void TetrahedralityParam::initializeHistogram() { |
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std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
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} |
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|
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void TetrahedralityParam::process() { |
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Molecule* mol; |
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StuntDouble* sd; |
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StuntDouble* sd2; |
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StuntDouble* sdi; |
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StuntDouble* sdj; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::IntegrableObjectIterator ioi; |
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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 cospsi; |
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RealType Qk; |
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std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; |
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int isd; |
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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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Distorted_.clear(); |
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Tetrahedral_.clear(); |
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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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|
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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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// update the positions of atoms which belong to the rigidbodies |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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|
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// outer loop is over the selected StuntDoubles: |
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|
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for (sd = seleMan_.beginSelected(isd); sd != NULL; |
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sd = seleMan_.nextSelected(isd)) { |
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|
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myIndex = sd->getGlobalIndex(); |
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Qk = 1.0; |
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|
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myNeighbors.clear(); |
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|
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// inner loop is over all StuntDoubles in the system: |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL; |
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sd2 = mol->nextIntegrableObject(ioi)) { |
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|
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if (sd2->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - sd2->getPos(); |
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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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r = vec.length(); |
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|
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// Check to see if neighbor is in bond cutoff |
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|
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if (r < rCut_) { |
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|
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myNeighbors.push_back(std::make_pair(r,sd2)); |
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} |
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} |
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} |
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} |
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|
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// Sort the vector using predicate and std::sort |
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std::sort(myNeighbors.begin(), myNeighbors.end()); |
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|
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//std::cerr << myNeighbors.size() << " neighbors within " |
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// << rCut_ << " A" << " \n"; |
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|
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// Use only the 4 closest neighbors to do the rest of the work: |
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|
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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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|
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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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|
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sdi = myNeighbors[i].second; |
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ri = sdi->getPos(); |
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rik = rk - ri; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rik); |
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|
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rik.normalize(); |
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|
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for (int j = i+1; j < nbors; j++) { |
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|
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sdj = myNeighbors[j].second; |
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rj = sdj->getPos(); |
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rkj = rk - rj; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rkj); |
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rkj.normalize(); |
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|
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cospsi = dot(rik,rkj); |
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|
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//std::cerr << "cos(psi) = " << cospsi << " \n"; |
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|
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// Calculates scaled Qk for each molecule using calculated |
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// 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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|
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// Saves positions of StuntDoubles & neighbors with distorted |
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// 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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|
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// Saves positions of StuntDoubles & neighbors with |
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// tetrahedral coordination (high Qk value) |
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if (Qk > 0.05) { |
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|
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Tetrahedral_.push_back(sd); |
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|
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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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} |
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} |
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|
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writeOrderParameter(); |
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std::cerr << "number of distorted StuntDoubles = " |
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<< Distorted_.size() << "\n"; |
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std::cerr << "number of tetrahedral StuntDoubles = " |
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<< Tetrahedral_.size() << "\n"; |
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} |
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|
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void TetrahedralityParam::collectHistogram(RealType Qk) { |
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|
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if (Qk > MinQ_ && Qk < MaxQ_) { |
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|
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int whichBin = int((Qk - MinQ_) / deltaQ_); |
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Q_histogram_[whichBin] += 1; |
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} |
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} |
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|
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|
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void TetrahedralityParam::writeOrderParameter() { |
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|
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int nSelected = 0; |
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|
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for (int i = 0; i < nBins_; ++i) { |
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nSelected = nSelected + int(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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|
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if (osq.is_open()) { |
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|
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osq << "# Tetrahedrality Parameters\n"; |
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osq << "# selection: (" << selectionScript_ << ")\n"; |
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osq << "# \n"; |
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < nBins_; ++i) { |
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RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
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osq << Qval; |
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osq << "\t" << (RealType) (Q_histogram_[i]/deltaQ_)/nSelected; |
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osq << "\n"; |
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} |
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|
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osq.close(); |
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|
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}else { |
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sprintf(painCave.errMsg, "TetrahedralityParam: unable to open %s\n", |
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(getOutputFileName() + "q").c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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|
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if (nFrames == 1) { |
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|
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std::vector<StuntDouble*>::iterator iter; |
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std::ofstream osd((getOutputFileName() + "dxyz").c_str()); |
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|
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if (osd.is_open()) { |
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|
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osd << Distorted_.size() << "\n"; |
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osd << "\n"; |
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|
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for (iter = Distorted_.begin(); iter != Distorted_.end(); ++iter) { |
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Vector3d position; |
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position = (*iter)->getPos(); |
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osd << "O " << "\t"; |
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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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} |
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osd << "\n"; |
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} |
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osd.close(); |
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} |
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|
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|
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std::ofstream ost((getOutputFileName() + "txyz").c_str()); |
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|
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if (ost.is_open()) { |
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|
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ost << Tetrahedral_.size() << "\n"; |
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ost << "\n"; |
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|
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for (iter = Tetrahedral_.begin(); iter != Tetrahedral_.end(); ++iter) { |
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Vector3d position; |
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position = (*iter)->getPos(); |
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|
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ost << "O " << "\t"; |
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|
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for (unsigned int z = 0; z < position.size(); z++) { |
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ost << position[z] << " " << "\t"; |
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} |
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ost << "\n"; |
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} |
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ost.close(); |
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} |
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} |
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} |
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} |
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