1 |
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/* |
2 |
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* 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 |
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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 |
27 |
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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 |
< |
* 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 |
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* University of Notre Dame has been advised of the possibility of |
39 |
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* such damages. |
40 |
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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), |
53 |
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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 -= 1.0/3.0 * Mat3x3d::identity(); |
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|
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Vector3d eigenvalues; |
137 |
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Mat3x3d eigenvectors; |
138 |
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Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
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|
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int which; |
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double 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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double 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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double 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(); |
159 |
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currentSnapshot_->wrapVector(vec); |
160 |
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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; |
170 |
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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(); |
176 |
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|
177 |
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} |
178 |
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|
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void P2OrderParameter::writeP2() { |
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|
181 |
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std::ofstream os(getOutputFileName().c_str()); |
182 |
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os << "#radial distribution function\n"; |
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os<< "#selection1: (" << selectionScript1_ << ")\t"; |
184 |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
185 |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
186 |
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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 |
> |
*/ |
41 |
> |
|
42 |
> |
#include "applications/staticProps/P2OrderParameter.hpp" |
43 |
> |
#include "utils/simError.h" |
44 |
> |
#include "io/DumpReader.hpp" |
45 |
> |
#include "primitives/Molecule.hpp" |
46 |
> |
#include "utils/NumericConstant.hpp" |
47 |
> |
namespace oopse { |
48 |
> |
|
49 |
> |
|
50 |
> |
P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
51 |
> |
: StaticAnalyser(info, filename), |
52 |
> |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
53 |
> |
seleMan1_(info), seleMan2_(info){ |
54 |
> |
|
55 |
> |
setOutputName(getPrefix(filename) + ".p2"); |
56 |
> |
|
57 |
> |
evaluator1_.loadScriptString(sele1); |
58 |
> |
evaluator2_.loadScriptString(sele2); |
59 |
> |
|
60 |
> |
if (!evaluator1_.isDynamic()) { |
61 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
62 |
> |
}else { |
63 |
> |
sprintf( painCave.errMsg, |
64 |
> |
"--sele1 must be static selection\n"); |
65 |
> |
painCave.severity = OOPSE_ERROR; |
66 |
> |
painCave.isFatal = 1; |
67 |
> |
simError(); |
68 |
> |
} |
69 |
> |
|
70 |
> |
if (!evaluator2_.isDynamic()) { |
71 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
72 |
> |
}else { |
73 |
> |
sprintf( painCave.errMsg, |
74 |
> |
"--sele2 must be static selection\n"); |
75 |
> |
painCave.severity = OOPSE_ERROR; |
76 |
> |
painCave.isFatal = 1; |
77 |
> |
simError(); |
78 |
> |
} |
79 |
> |
|
80 |
> |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
81 |
> |
sprintf( painCave.errMsg, |
82 |
> |
"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
83 |
> |
painCave.severity = OOPSE_ERROR; |
84 |
> |
painCave.isFatal = 1; |
85 |
> |
simError(); |
86 |
> |
|
87 |
> |
} |
88 |
> |
|
89 |
> |
int i; |
90 |
> |
int j; |
91 |
> |
StuntDouble* sd1; |
92 |
> |
StuntDouble* sd2; |
93 |
> |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); |
94 |
> |
sd1 != NULL && sd2 != NULL; |
95 |
> |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
96 |
> |
|
97 |
> |
sdPairs_.push_back(std::make_pair(sd1, sd2)); |
98 |
> |
} |
99 |
> |
|
100 |
> |
|
101 |
> |
} |
102 |
> |
|
103 |
> |
void P2OrderParameter::process() { |
104 |
> |
Molecule* mol; |
105 |
> |
RigidBody* rb; |
106 |
> |
SimInfo::MoleculeIterator mi; |
107 |
> |
Molecule::RigidBodyIterator rbIter; |
108 |
> |
|
109 |
> |
DumpReader reader(info_, dumpFilename_); |
110 |
> |
int nFrames = reader.getNFrames(); |
111 |
> |
|
112 |
> |
for (int i = 0; i < nFrames; i += step_) { |
113 |
> |
reader.readFrame(i); |
114 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
115 |
> |
|
116 |
> |
|
117 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
118 |
> |
//change the positions of atoms which belong to the rigidbodies |
119 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
120 |
> |
rb->updateAtoms(); |
121 |
> |
} |
122 |
> |
|
123 |
> |
} |
124 |
> |
|
125 |
> |
Mat3x3d orderTensor(0.0); |
126 |
> |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
127 |
> |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
128 |
> |
if (usePeriodicBoundaryConditions_) |
129 |
> |
currentSnapshot_->wrapVector(vec); |
130 |
> |
vec.normalize(); |
131 |
> |
orderTensor +=outProduct(vec, vec); |
132 |
> |
} |
133 |
> |
|
134 |
> |
orderTensor /= sdPairs_.size(); |
135 |
> |
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
136 |
> |
|
137 |
> |
Vector3d eigenvalues; |
138 |
> |
Mat3x3d eigenvectors; |
139 |
> |
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
140 |
> |
|
141 |
> |
int which; |
142 |
> |
RealType maxEval = 0.0; |
143 |
> |
for(int k = 0; k< 3; k++){ |
144 |
> |
if(fabs(eigenvalues[k]) > maxEval){ |
145 |
> |
which = k; |
146 |
> |
maxEval = fabs(eigenvalues[k]); |
147 |
> |
} |
148 |
> |
} |
149 |
> |
RealType p2 = 1.5 * maxEval; |
150 |
> |
|
151 |
> |
//the eigen vector is already normalized in SquareMatrix3::diagonalize |
152 |
> |
Vector3d director = eigenvectors.getColumn(which); |
153 |
> |
if (director[0] < 0) { |
154 |
> |
director.negate(); |
155 |
> |
} |
156 |
> |
|
157 |
> |
RealType angle = 0.0; |
158 |
> |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
159 |
> |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
160 |
> |
if (usePeriodicBoundaryConditions_) |
161 |
> |
currentSnapshot_->wrapVector(vec); |
162 |
> |
vec.normalize(); |
163 |
> |
|
164 |
> |
angle += acos(dot(vec, director)) ; |
165 |
> |
} |
166 |
> |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
167 |
> |
|
168 |
> |
OrderParam param; |
169 |
> |
param.p2 = p2; |
170 |
> |
param.director = director; |
171 |
> |
param.angle = angle; |
172 |
> |
|
173 |
> |
orderParams_.push_back(param); |
174 |
> |
|
175 |
> |
} |
176 |
> |
|
177 |
> |
writeP2(); |
178 |
> |
|
179 |
> |
} |
180 |
> |
|
181 |
> |
void P2OrderParameter::writeP2() { |
182 |
> |
|
183 |
> |
std::ofstream os(getOutputFileName().c_str()); |
184 |
> |
os << "#radial distribution function\n"; |
185 |
> |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
186 |
> |
os << "selection2: (" << selectionScript2_ << ")\n"; |
187 |
> |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
188 |
> |
|
189 |
> |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
190 |
> |
os << orderParams_[i].p2 << "\t" |
191 |
> |
<< orderParams_[i].director[0] << "\t" |
192 |
> |
<< orderParams_[i].director[1] << "\t" |
193 |
> |
<< orderParams_[i].director[2] << "\t" |
194 |
> |
<< orderParams_[i].angle << "\n"; |
195 |
> |
|
196 |
> |
} |
197 |
> |
|
198 |
> |
} |
199 |
> |
|
200 |
> |
} |
201 |
> |
|