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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. 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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* 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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* 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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|
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#include "applications/staticProps/P2OrderParameter.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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namespace oopse { |
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|
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info){ |
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|
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setOutputName(getPrefix(filename) + ".p2"); |
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|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"--sele1 must be static selection\n"); |
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painCave.severity = OOPSE_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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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"--sele2 must be static selection\n"); |
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painCave.severity = OOPSE_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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if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
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sprintf( painCave.errMsg, |
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"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
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painCave.severity = OOPSE_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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|
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int i; |
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int j; |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
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|
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sdPairs_.push_back(std::make_pair(sd1, 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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void P2OrderParameter::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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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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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; 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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Mat3x3d orderTensor(0.0); |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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orderTensor +=outProduct(vec, vec); |
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} |
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|
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orderTensor /= sdPairs_.size(); |
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orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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|
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Vector3d eigenvalues; |
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Mat3x3d eigenvectors; |
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Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
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|
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int which; |
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RealType maxEval = 0.0; |
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for(int k = 0; k< 3; k++){ |
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if(fabs(eigenvalues[k]) > maxEval){ |
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which = k; |
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maxEval = fabs(eigenvalues[k]); |
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} |
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} |
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RealType p2 = 1.5 * maxEval; |
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|
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//the eigen vector is already normalized in SquareMatrix3::diagonalize |
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Vector3d director = eigenvectors.getColumn(which); |
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if (director[0] < 0) { |
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director.negate(); |
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} |
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|
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RealType angle = 0.0; |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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|
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angle += acos(dot(vec, director)) ; |
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} |
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angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
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|
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OrderParam param; |
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param.p2 = p2; |
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param.director = director; |
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param.angle = angle; |
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|
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orderParams_.push_back(param); |
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|
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} |
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|
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writeP2(); |
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|
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} |
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|
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void P2OrderParameter::writeP2() { |
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|
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std::ofstream os(getOutputFileName().c_str()); |
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os << "#radial distribution function\n"; |
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os<< "#selection1: (" << selectionScript1_ << ")\t"; |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
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|
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for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
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os << orderParams_[i].p2 << "\t" |
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<< orderParams_[i].director[0] << "\t" |
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<< orderParams_[i].director[1] << "\t" |
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<< orderParams_[i].director[2] << "\t" |
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<< orderParams_[i].angle << "\n"; |
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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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|
