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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
< |
* |
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< |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
< |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
< |
* redistribute this software in source and binary code form, provided |
| 7 |
< |
* that the following conditions are met: |
| 8 |
< |
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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* 2. Redistributions of source code must retain the above copyright |
| 19 |
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* notice, this list of conditions and the following disclaimer. |
| 20 |
< |
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
< |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
< |
* documentation and/or other materials provided with the |
| 24 |
< |
* distribution. |
| 25 |
< |
* |
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* This software is provided "AS IS," without a warranty of any |
| 27 |
< |
* kind. All express or implied conditions, representations and |
| 28 |
< |
* warranties, including any implied warranty of merchantability, |
| 29 |
< |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
< |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
< |
* be liable for any damages suffered by licensee as a result of |
| 32 |
< |
* using, modifying or distributing the software or its |
| 33 |
< |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
< |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
< |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
< |
* damages, however caused and regardless of the theory of liability, |
| 37 |
< |
* arising out of the use of or inability to use software, even if the |
| 38 |
< |
* University of Notre Dame has been advised of the possibility of |
| 39 |
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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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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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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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|
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> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
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> |
|
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|
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/* Creates orientational bond order parameters as outlined by |
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
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* Phys Rev B, 28,784,1983 |
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* |
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*/ |
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|
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#include "applications/staticProps/BondOrderParameter.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 "math/RealSphericalHarmonic.hpp" |
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> |
namespace oopse { |
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|
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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 lNumber, int nbins) |
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> |
: StaticAnalyser(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info){ |
| 64 |
> |
|
| 65 |
> |
setOutputName(getPrefix(filename) + ".obo"); |
| 66 |
> |
|
| 67 |
> |
evaluator_.loadScriptString(sele); |
| 68 |
> |
if (!evaluator_.isDynamic()) { |
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> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 70 |
> |
} |
| 71 |
> |
|
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// Set up cutoff radius and order of the Legendre Polynomial: |
| 73 |
> |
|
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lNumber_ = lNumber; |
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> |
rCut_ = rCut; |
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> |
mSize_ = 2*lNumber_+1; |
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> |
|
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> |
deltaQ_ = 1.0 / nbins; |
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> |
deltaW_ = 2.0 / nbins; |
| 80 |
> |
|
| 81 |
> |
Q_histogram_.resize(nbins); |
| 82 |
> |
W_histogram_.resize(nbins); |
| 83 |
> |
|
| 84 |
> |
} |
| 85 |
> |
|
| 86 |
> |
void BondOrderParameter::initalizeHistogram() { |
| 87 |
> |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
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> |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
| 89 |
> |
} |
| 90 |
> |
|
| 91 |
> |
void BondOrderParameter::process() { |
| 92 |
> |
Molecule* mol; |
| 93 |
> |
Atom* atom; |
| 94 |
> |
RigidBody* rb; |
| 95 |
> |
SimInfo::MoleculeIterator mi; |
| 96 |
> |
Molecule::RigidBodyIterator rbIter; |
| 97 |
> |
Molecule::AtomIterator ai; |
| 98 |
> |
StuntDouble* sd; |
| 99 |
> |
RealType theta; |
| 100 |
> |
RealType phi; |
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> |
RealType r; |
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> |
RealType dist; |
| 103 |
> |
std::map<int, RealType> QBar_lm; |
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> |
RealType QSq_l; |
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> |
RealType Q_l; |
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> |
int nBonds; |
| 107 |
> |
RealSphericalHarmonic sphericalHarmonic; |
| 108 |
> |
int i, j; |
| 109 |
> |
|
| 110 |
> |
// Set the l for the spherical harmonic, it doesn't change |
| 111 |
> |
sphericalHarmonic.setL(lNumber_); |
| 112 |
> |
|
| 113 |
> |
|
| 114 |
> |
DumpReader reader(info_, dumpFilename_); |
| 115 |
> |
int nFrames = reader.getNFrames(); |
| 116 |
> |
|
| 117 |
> |
|
| 118 |
> |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 119 |
> |
reader.readFrame(istep); |
| 120 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 121 |
> |
|
| 122 |
> |
if (evaluator_.isDynamic()) { |
| 123 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 124 |
> |
} |
| 125 |
> |
|
| 126 |
> |
// update the positions of atoms which belong to the rigidbodies |
| 127 |
> |
|
| 128 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 129 |
> |
mol = info_->nextMolecule(mi)) { |
| 130 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 131 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 132 |
> |
rb->updateAtoms(); |
| 133 |
> |
} |
| 134 |
> |
} |
| 135 |
> |
|
| 136 |
> |
// outer loop is over the selected StuntDoubles: |
| 137 |
> |
|
| 138 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 139 |
> |
sd = seleMan_.nextSelected(i)) { |
| 140 |
> |
|
| 141 |
> |
// For this central atom, zero out nBonds and QBar_lm |
| 142 |
> |
|
| 143 |
> |
nBonds = 0; |
| 144 |
> |
|
| 145 |
> |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 146 |
> |
QBar_lm[m] = 0.0; |
| 147 |
> |
} |
| 148 |
> |
|
| 149 |
> |
// inner loop is over all other atoms in the system: |
| 150 |
> |
|
| 151 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 152 |
> |
mol = info_->nextMolecule(mi)) { |
| 153 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 154 |
> |
atom = mol->nextAtom(ai)) { |
| 155 |
> |
|
| 156 |
> |
|
| 157 |
> |
Vector3d vec = sd->getPos() - atom->getPos(); |
| 158 |
> |
currentSnapshot_->wrapVector(vec); |
| 159 |
> |
|
| 160 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 161 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 162 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 163 |
> |
// system, we choose standard spherical coordinates |
| 164 |
> |
|
| 165 |
> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 166 |
> |
|
| 167 |
> |
// Check to see if neighbor is in bond cutoff |
| 168 |
> |
|
| 169 |
> |
if (r < rCut_) { |
| 170 |
> |
theta = atan2(vec.y(), vec.x()); |
| 171 |
> |
phi = acos(vec.z()/r); |
| 172 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 173 |
> |
sphericalHarmonic.setM(m); |
| 174 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
| 175 |
> |
} |
| 176 |
> |
nBonds++; |
| 177 |
> |
} |
| 178 |
> |
} |
| 179 |
> |
} |
| 180 |
> |
|
| 181 |
> |
// Normalize Qbar |
| 182 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 183 |
> |
QBar_lm[m] /= nBonds; |
| 184 |
> |
} |
| 185 |
> |
|
| 186 |
> |
// Find second order invariant Q_l |
| 187 |
> |
|
| 188 |
> |
QSq_l = 0.0; |
| 189 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 190 |
> |
QSq_l += pow(QBar_lm[m], 2); |
| 191 |
> |
} |
| 192 |
> |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
| 193 |
> |
|
| 194 |
> |
// Find Third Order Invariant W_l |
| 195 |
> |
|
| 196 |
> |
// Make arrays for Wigner3jm |
| 197 |
> |
double* THRCOF = new double[mSize_]; |
| 198 |
> |
// Variables for Wigner routine |
| 199 |
> |
double l_ = (double)lNumber_; |
| 200 |
> |
double m2Min, m2Max; |
| 201 |
> |
int error, m1, m2, m3; |
| 202 |
> |
|
| 203 |
> |
RealType W_l; |
| 204 |
> |
RealType W_l_hat; |
| 205 |
> |
W_l = 0.0; |
| 206 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 207 |
> |
// Zero work array |
| 208 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
| 209 |
> |
THRCOF[i] = 0.0; |
| 210 |
> |
} |
| 211 |
> |
// Get Wigner coefficients |
| 212 |
> |
Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
| 213 |
> |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
| 214 |
> |
m2 = floor(m2Min) + m_index - 1; |
| 215 |
> |
m3 = -m1-m2; |
| 216 |
> |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
| 217 |
> |
} |
| 218 |
> |
} |
| 219 |
> |
|
| 220 |
> |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 221 |
> |
|
| 222 |
> |
// accumulate histogram data for Q_l and W_l_hat: |
| 223 |
> |
|
| 224 |
> |
collectHistogram(Q_l, W_l_hat); |
| 225 |
> |
|
| 226 |
> |
} |
| 227 |
> |
} |
| 228 |
> |
|
| 229 |
> |
// Normalize by number of frames |
| 230 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 231 |
> |
QBar_lm[m] /= nFrames; |
| 232 |
> |
} |
| 233 |
> |
|
| 234 |
> |
|
| 235 |
> |
|
| 236 |
> |
|
| 237 |
> |
|
| 238 |
> |
writeOrderParameter(); |
| 239 |
> |
|
| 240 |
> |
} |
| 241 |
> |
|
| 242 |
> |
|
| 243 |
> |
void BondOrderParameter::processHistogram() { |
| 244 |
> |
|
| 245 |
> |
int nPairs = getNPairs(); |
| 246 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 247 |
> |
RealType pairDensity = nPairs /volume * 2.0; |
| 248 |
> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 249 |
> |
|
| 250 |
> |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 251 |
> |
|
| 252 |
> |
RealType rLower = i * deltaR_; |
| 253 |
> |
RealType rUpper = rLower + deltaR_; |
| 254 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 255 |
> |
RealType nIdeal = volSlice * pairConstant; |
| 256 |
> |
|
| 257 |
> |
avgGofr_[i] += histogram_[i] / nIdeal; |
| 258 |
> |
} |
| 259 |
> |
|
| 260 |
> |
} |
| 261 |
> |
|
| 262 |
> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
| 263 |
> |
|
| 264 |
> |
if (Q_l < MaxQ_) { |
| 265 |
> |
int whichBin = Q_l / deltaQ_; |
| 266 |
> |
Q_histogram_[whichBin] += 1; |
| 267 |
> |
} |
| 268 |
> |
if (W_l_hat < MaxW_) { |
| 269 |
> |
int whichBin = W_l_hat / deltaW_; |
| 270 |
> |
W_histogram_[whichBin] += 1; |
| 271 |
> |
} |
| 272 |
> |
} |
| 273 |
> |
|
| 274 |
> |
|
| 275 |
> |
void BondOrderParameter::writeOrderParameter() { |
| 276 |
> |
|
| 277 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 278 |
> |
os << "#Bond Order Parameter\n"; |
| 279 |
> |
os << "#selection: (" << selectionScript_ << ")\n"; |
| 280 |
> |
|
| 281 |
> |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 282 |
> |
os << orderParams_[i].p2 << "\t" |
| 283 |
> |
<< orderParams_[i].director[0] << "\t" |
| 284 |
> |
<< orderParams_[i].director[1] << "\t" |
| 285 |
> |
<< orderParams_[i].director[2] << "\t" |
| 286 |
> |
<< orderParams_[i].angle << "\n"; |
| 287 |
> |
|
| 288 |
> |
} |
| 289 |
> |
} |
| 290 |
> |
|
| 291 |
> |
|
| 292 |
> |
|
| 293 |
> |
} |
