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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
5 |
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* non-exclusive, royalty free, license to use, modify and |
6 |
< |
* redistribute this software in source and binary code form, provided |
7 |
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* that the following conditions are met: |
8 |
< |
* |
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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 |
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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
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* |
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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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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
22 |
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* notice, this list of conditions and the following disclaimer in the |
23 |
< |
* documentation and/or other materials provided with the |
24 |
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* distribution. |
25 |
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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 |
28 |
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* warranties, including any implied warranty of merchantability, |
29 |
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* 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 |
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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/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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namespace oopse { |
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|
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double rCut, int lNumber) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), evaluator1_(info), |
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seleMan1_(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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|
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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 = seleMan1_.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 BondOrderParameter::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 BondOrderParameter::writeOrderParameter() { |
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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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|
1 |
> |
/* |
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/SphericalHarmonic.hpp" |
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|
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namespace oopse { |
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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) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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|
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setOutputName(getPrefix(filename) + ".bo"); |
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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 and order of the Legendre Polynomial: |
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|
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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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// Q can take values from 0 to 1 |
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|
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MinQ_ = 0.0; |
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MaxQ_ = 1.0; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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Q_histogram_.resize(nbins); |
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|
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
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|
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MinW_ = -0.18; |
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MaxW_ = 0.18; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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W_histogram_.resize(nbins); |
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|
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} |
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|
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BondOrderParameter::~BondOrderParameter() { |
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Q_histogram_.clear(); |
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W_histogram_.clear(); |
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} |
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|
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void BondOrderParameter::initalizeHistogram() { |
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std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
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std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
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} |
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|
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void BondOrderParameter::process() { |
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Molecule* mol; |
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Atom* atom; |
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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::AtomIterator ai; |
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StuntDouble* sd; |
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Vector3d vec; |
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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<int, ComplexType> QBar_lm; |
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RealType QSq_l; |
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RealType Q_l; |
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ComplexType W_l; |
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ComplexType W_l_hat; |
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int nBonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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// Make arrays for Wigner3jm |
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> |
double* THRCOF = new double[mSize_]; |
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> |
// Variables for Wigner routine |
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double l_ = (double)lNumber_; |
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double m1Pass, m2Min, m2Max; |
130 |
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int error, m1, m2, m3; |
131 |
> |
|
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// Set the l for the spherical harmonic, it doesn't change |
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sphericalHarmonic.setL(lNumber_); |
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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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for (int istep = 0; istep < nFrames; istep += step_) { |
140 |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
143 |
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|
144 |
> |
if (evaluator_.isDynamic()) { |
145 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
146 |
> |
} |
147 |
> |
|
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> |
// update the positions of atoms which belong to the rigidbodies |
149 |
> |
|
150 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
151 |
> |
mol = info_->nextMolecule(mi)) { |
152 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
153 |
> |
rb = mol->nextRigidBody(rbIter)) { |
154 |
> |
rb->updateAtoms(); |
155 |
> |
} |
156 |
> |
} |
157 |
> |
|
158 |
> |
// outer loop is over the selected StuntDoubles: |
159 |
> |
|
160 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
161 |
> |
sd = seleMan_.nextSelected(i)) { |
162 |
> |
|
163 |
> |
myIndex = sd->getGlobalIndex(); |
164 |
> |
|
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// For this central atom, zero out nBonds and QBar_lm |
166 |
> |
|
167 |
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nBonds = 0; |
168 |
> |
|
169 |
> |
for (int m = -lNumber_; m <= lNumber_; m++) { |
170 |
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QBar_lm[m] = 0.0; |
171 |
> |
} |
172 |
> |
|
173 |
> |
// inner loop is over all other atoms in the system: |
174 |
> |
|
175 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
176 |
> |
mol = info_->nextMolecule(mi)) { |
177 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
178 |
> |
atom = mol->nextAtom(ai)) { |
179 |
> |
|
180 |
> |
if (atom->getGlobalIndex() != myIndex) { |
181 |
> |
|
182 |
> |
vec = sd->getPos() - atom->getPos(); |
183 |
> |
currentSnapshot_->wrapVector(vec); |
184 |
> |
|
185 |
> |
// Calculate "bonds" and build Q_lm(r) where |
186 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
187 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
188 |
> |
// system, we choose standard spherical coordinates |
189 |
> |
|
190 |
> |
r = vec.length(); |
191 |
> |
|
192 |
> |
// Check to see if neighbor is in bond cutoff |
193 |
> |
|
194 |
> |
if (r < rCut_) { |
195 |
> |
costheta = vec.z() / r; |
196 |
> |
phi = atan2(vec.y(), vec.x()); |
197 |
> |
|
198 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
199 |
> |
sphericalHarmonic.setM(m); |
200 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
201 |
> |
} |
202 |
> |
nBonds++; |
203 |
> |
} |
204 |
> |
} |
205 |
> |
} |
206 |
> |
} |
207 |
> |
|
208 |
> |
// Normalize Qbar2 |
209 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
210 |
> |
QBar_lm[m] /= nBonds; |
211 |
> |
std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; |
212 |
> |
} |
213 |
> |
|
214 |
> |
// Find second order invariant Q_l |
215 |
> |
|
216 |
> |
QSq_l = 0.0; |
217 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
218 |
> |
QSq_l += norm(QBar_lm[m]); |
219 |
> |
} |
220 |
> |
std::cout << "qsq_l = " << QSq_l << "\n"; |
221 |
> |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
222 |
> |
|
223 |
> |
// Find Third Order Invariant W_l |
224 |
> |
|
225 |
> |
W_l = 0.0; |
226 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
227 |
> |
// Zero work array |
228 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
229 |
> |
THRCOF[i] = 0.0; |
230 |
> |
} |
231 |
> |
// Get Wigner coefficients |
232 |
> |
m1Pass = (double)m1; |
233 |
> |
Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
234 |
> |
for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) { |
235 |
> |
m2 = floor(m2Min) + m_index - 1; |
236 |
> |
m3 = -m1-m2; |
237 |
> |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
238 |
> |
} |
239 |
> |
} |
240 |
> |
|
241 |
> |
W_l_hat = W_l / pow(QSq_l, 1.5); |
242 |
> |
|
243 |
> |
// accumulate histogram data for Q_l and W_l_hat: |
244 |
> |
|
245 |
> |
std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; |
246 |
> |
collectHistogram(Q_l, real(W_l_hat)); |
247 |
> |
|
248 |
> |
} |
249 |
> |
} |
250 |
> |
|
251 |
> |
writeOrderParameter(); |
252 |
> |
|
253 |
> |
} |
254 |
> |
|
255 |
> |
|
256 |
> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
257 |
> |
|
258 |
> |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
259 |
> |
int qbin = (Q_l - MinQ_) / deltaQ_; |
260 |
> |
Q_histogram_[qbin] += 1; |
261 |
> |
Qcount_++; |
262 |
> |
sumQ_ += Q_l; |
263 |
> |
sumQ2_ += Q_l * Q_l; |
264 |
> |
} else { |
265 |
> |
sprintf( painCave.errMsg, |
266 |
> |
"Q_l value outside reasonable range\n"); |
267 |
> |
painCave.severity = OOPSE_ERROR; |
268 |
> |
painCave.isFatal = 1; |
269 |
> |
simError(); |
270 |
> |
} |
271 |
> |
|
272 |
> |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
273 |
> |
int wbin = (W_l_hat - MinW_) / deltaW_; |
274 |
> |
W_histogram_[wbin] += 1; |
275 |
> |
Wcount_++; |
276 |
> |
sumW_ += W_l_hat; |
277 |
> |
sumW2_ += W_l_hat*W_l_hat; |
278 |
> |
} else { |
279 |
> |
sprintf( painCave.errMsg, |
280 |
> |
"W_l_hat value outside reasonable range\n"); |
281 |
> |
painCave.severity = OOPSE_ERROR; |
282 |
> |
painCave.isFatal = 1; |
283 |
> |
simError(); |
284 |
> |
} |
285 |
> |
} |
286 |
> |
|
287 |
> |
void BondOrderParameter::writeOrderParameter() { |
288 |
> |
|
289 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
290 |
> |
|
291 |
> |
if (osq.is_open()) { |
292 |
> |
|
293 |
> |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
294 |
> |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
295 |
> |
|
296 |
> |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
297 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
298 |
> |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
299 |
> |
osq << "# std. dev.: " << qStdDev << "\n"; |
300 |
> |
|
301 |
> |
// Normalize by number of frames and write it out: |
302 |
> |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
303 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
304 |
> |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
305 |
> |
} |
306 |
> |
|
307 |
> |
osq.close(); |
308 |
> |
} else { |
309 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
310 |
> |
(getOutputFileName() + "q").c_str()); |
311 |
> |
painCave.isFatal = 1; |
312 |
> |
simError(); |
313 |
> |
} |
314 |
> |
|
315 |
> |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
316 |
> |
|
317 |
> |
if (osw.is_open()) { |
318 |
> |
|
319 |
> |
RealType wAvg = sumW_ / (RealType) Wcount_; |
320 |
> |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
321 |
> |
|
322 |
> |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
323 |
> |
osw << "# selection: (" << selectionScript_ << ")\n"; |
324 |
> |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
325 |
> |
osw << "# std. dev.: " << wStdDev << "\n"; |
326 |
> |
|
327 |
> |
// Normalize by number of frames and write it out: |
328 |
> |
for (int i = 0; i < W_histogram_.size(); ++i) { |
329 |
> |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
330 |
> |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
331 |
> |
} |
332 |
> |
|
333 |
> |
osw.close(); |
334 |
> |
} else { |
335 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
336 |
> |
(getOutputFileName() + "w").c_str()); |
337 |
> |
painCave.isFatal = 1; |
338 |
> |
simError(); |
339 |
> |
} |
340 |
> |
} |
341 |
> |
} |