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/* |
| 2 |
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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 |
< |
* |
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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 |
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* the article in which the program was described (Matthew |
| 13 |
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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)) |
| 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. |
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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 |
< |
* 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 |
< |
* warranties, including any implied warranty of merchantability, |
| 29 |
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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 |
| 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 |
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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 |
| 39 |
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* such damages. |
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*/ |
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|
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#include "applications/staticProps/SCDOrderParameter.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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SCDElem::SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, |
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const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){ |
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SelectionManager seleMan1_(info); |
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SelectionManager seleMan2_(info); |
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SelectionManager seleMan3_(info); |
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SelectionEvaluator evaluator1_(info); |
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SelectionEvaluator evaluator2_(info); |
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SelectionEvaluator evaluator3_(info); |
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|
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evaluator1_.loadScriptString(sele1_); |
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evaluator2_.loadScriptString(sele2_); |
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evaluator3_.loadScriptString(sele3_); |
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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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"dynamic selection is not allowed\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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"dynamic selection is not allowed\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 (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"dynamic selection is not allowed\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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int nselected1 = seleMan1_.getSelectionCount(); |
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int nselected2 = seleMan2_.getSelectionCount(); |
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int nselected3 = seleMan3_.getSelectionCount(); |
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|
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if ( nselected1 != nselected2 || nselected1 != nselected3 ) { |
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sprintf( painCave.errMsg, |
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"The number of selected Stuntdoubles must be the same\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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int i; |
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int j; |
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int k; |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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StuntDouble* sd3; |
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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k); |
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sd1 != NULL && sd2 != NULL && sd3 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) { |
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tuples_.push_back(make_tuple3(sd1, sd2, sd3)); |
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} |
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|
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} |
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|
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double SCDElem::calcSCD(Snapshot* snapshot) { |
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std::vector<SDTuple3>::iterator i; |
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Vector3d normal(0.0, 0.0, 1.0); |
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double scd = 0.0; |
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for (i = tuples_.begin(); i != tuples_.end(); ++i) { |
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Vector3d zAxis = i->third->getPos() - i->first->getPos(); |
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snapshot->wrapVector(zAxis); |
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Vector3d v12 = i->second->getPos() - i->first->getPos(); |
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snapshot->wrapVector(v12); |
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Vector3d xAxis = cross(v12, zAxis); |
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Vector3d yAxis = cross(zAxis, xAxis); |
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|
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xAxis.normalize(); |
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yAxis.normalize(); |
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zAxis.normalize(); |
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double cosThetaX = dot(xAxis, normal); |
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double sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0); |
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double cosThetaY = dot(yAxis, normal); |
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double syy = 0.5*(3*cosThetaY * cosThetaY - 1.0); |
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scd += 2.0/3.0*sxx + 1.0/3.0*syy; |
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} |
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scd /= tuples_.size(); |
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return scd; |
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|
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} |
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|
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SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& sele1, const std::string& sele2, const std::string& sele3) |
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: StaticAnalyser(info, filename) { |
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|
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setOutputName(getPrefix(filename) + ".scd"); |
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|
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scdElems_.push_back(SCDElem(info, sele1, sele2, sele3)); |
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scdParam_.resize(scdElems_.size()); |
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std::fill(scdParam_.begin(), scdParam_.end(), 0.0); |
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|
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} |
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|
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SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& molname, int beginIndex, int endIndex) |
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: StaticAnalyser(info, filename) { |
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|
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setOutputName(getPrefix(filename) + ".scd"); |
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|
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assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2); |
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for (int i = beginIndex; i <= endIndex -2 ; ++i) { |
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std::string selectionTemplate = "select " + molname + "."; |
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std::string sele1 = selectionTemplate + OOPSE_itoa(i); |
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std::string sele2 = selectionTemplate + OOPSE_itoa(i+1); |
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std::string sele3 = selectionTemplate + OOPSE_itoa(i+2); |
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|
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scdElems_.push_back(SCDElem(info, sele1, sele2, sele3)); |
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} |
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|
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scdParam_.resize(scdElems_.size()); |
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std::fill(scdParam_.begin(), scdParam_.end(), 0.0); |
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} |
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|
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|
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void SCDOrderParameter::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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for (std::size_t j = 0; j < scdElems_.size(); ++j) { |
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scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_); |
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} |
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|
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} |
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|
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int nProcessed = nFrames /step_; |
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for (std::size_t j = 0; j < scdElems_.size(); ++j) { |
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scdParam_[j] /= nProcessed; |
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} |
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|
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writeSCD(); |
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|
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< |
} |
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|
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< |
void SCDOrderParameter::writeSCD() { |
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|
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std::ofstream os(getOutputFileName().c_str()); |
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os << "#scd parameter\n"; |
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< |
for (std::size_t i = 0; i < scdElems_.size(); ++i) { |
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os << "#[column " << i+1 << "]\t" |
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<< "sele1: \"" << scdElems_[i].getSelection1() << "\",\t" |
| 221 |
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<< "sele2: \"" << scdElems_[i].getSelection2() << "\",\t" |
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<< "sele3: \"" << scdElems_[i].getSelection3() << "\"\n"; |
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< |
} |
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< |
|
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< |
for (std::size_t i = 0; i < scdElems_.size(); ++i) { |
| 226 |
< |
os << scdParam_[i]<< "\t"; |
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< |
} |
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< |
os << std::endl; |
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< |
} |
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|
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|
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} |
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|
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|
| 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. Redistributions of source code must retain the above copyright |
| 10 |
> |
* notice, this list of conditions and the following disclaimer. |
| 11 |
> |
* |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
> |
* documentation and/or other materials provided with the |
| 15 |
> |
* distribution. |
| 16 |
> |
* |
| 17 |
> |
* This software is provided "AS IS," without a warranty of any |
| 18 |
> |
* kind. All express or implied conditions, representations and |
| 19 |
> |
* warranties, including any implied warranty of merchantability, |
| 20 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
> |
* be liable for any damages suffered by licensee as a result of |
| 23 |
> |
* using, modifying or distributing the software or its |
| 24 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
> |
* damages, however caused and regardless of the theory of liability, |
| 28 |
> |
* arising out of the use of or inability to use software, even if the |
| 29 |
> |
* University of Notre Dame has been advised of the possibility of |
| 30 |
> |
* such damages. |
| 31 |
> |
* |
| 32 |
> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
> |
* research, please cite the appropriate papers when you publish your |
| 34 |
> |
* work. Good starting points are: |
| 35 |
> |
* |
| 36 |
> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
> |
*/ |
| 42 |
> |
|
| 43 |
> |
#include "applications/staticProps/SCDOrderParameter.hpp" |
| 44 |
> |
#include "utils/simError.h" |
| 45 |
> |
#include "io/DumpReader.hpp" |
| 46 |
> |
#include "primitives/Molecule.hpp" |
| 47 |
> |
#include "utils/NumericConstant.hpp" |
| 48 |
> |
namespace OpenMD { |
| 49 |
> |
|
| 50 |
> |
SCDElem::SCDElem(SimInfo* info, const std::string& sele1, |
| 51 |
> |
const std::string& sele2, const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){ |
| 52 |
> |
|
| 53 |
> |
usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 54 |
> |
|
| 55 |
> |
SelectionManager seleMan1_(info); |
| 56 |
> |
SelectionManager seleMan2_(info); |
| 57 |
> |
SelectionManager seleMan3_(info); |
| 58 |
> |
SelectionEvaluator evaluator1_(info); |
| 59 |
> |
SelectionEvaluator evaluator2_(info); |
| 60 |
> |
SelectionEvaluator evaluator3_(info); |
| 61 |
> |
|
| 62 |
> |
evaluator1_.loadScriptString(sele1_); |
| 63 |
> |
evaluator2_.loadScriptString(sele2_); |
| 64 |
> |
evaluator3_.loadScriptString(sele3_); |
| 65 |
> |
|
| 66 |
> |
if (!evaluator1_.isDynamic()) { |
| 67 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 68 |
> |
}else { |
| 69 |
> |
sprintf( painCave.errMsg, |
| 70 |
> |
"dynamic selection is not allowed\n"); |
| 71 |
> |
painCave.severity = OPENMD_ERROR; |
| 72 |
> |
painCave.isFatal = 1; |
| 73 |
> |
simError(); |
| 74 |
> |
} |
| 75 |
> |
|
| 76 |
> |
if (!evaluator2_.isDynamic()) { |
| 77 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 78 |
> |
}else { |
| 79 |
> |
sprintf( painCave.errMsg, |
| 80 |
> |
"dynamic selection is not allowed\n"); |
| 81 |
> |
painCave.severity = OPENMD_ERROR; |
| 82 |
> |
painCave.isFatal = 1; |
| 83 |
> |
simError(); |
| 84 |
> |
} |
| 85 |
> |
|
| 86 |
> |
if (!evaluator3_.isDynamic()) { |
| 87 |
> |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 88 |
> |
}else { |
| 89 |
> |
sprintf( painCave.errMsg, |
| 90 |
> |
"dynamic selection is not allowed\n"); |
| 91 |
> |
painCave.severity = OPENMD_ERROR; |
| 92 |
> |
painCave.isFatal = 1; |
| 93 |
> |
simError(); |
| 94 |
> |
} |
| 95 |
> |
|
| 96 |
> |
int nselected1 = seleMan1_.getSelectionCount(); |
| 97 |
> |
int nselected2 = seleMan2_.getSelectionCount(); |
| 98 |
> |
int nselected3 = seleMan3_.getSelectionCount(); |
| 99 |
> |
|
| 100 |
> |
if ( nselected1 != nselected2 || nselected1 != nselected3 ) { |
| 101 |
> |
sprintf( painCave.errMsg, |
| 102 |
> |
"The number of selected Stuntdoubles must be the same\n"); |
| 103 |
> |
painCave.severity = OPENMD_ERROR; |
| 104 |
> |
painCave.isFatal = 1; |
| 105 |
> |
simError(); |
| 106 |
> |
} |
| 107 |
> |
|
| 108 |
> |
int i; |
| 109 |
> |
int j; |
| 110 |
> |
int k; |
| 111 |
> |
StuntDouble* sd1; |
| 112 |
> |
StuntDouble* sd2; |
| 113 |
> |
StuntDouble* sd3; |
| 114 |
> |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k); |
| 115 |
> |
sd1 != NULL && sd2 != NULL && sd3 != NULL; |
| 116 |
> |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) { |
| 117 |
> |
tuples_.push_back(make_tuple3(sd1, sd2, sd3)); |
| 118 |
> |
} |
| 119 |
> |
|
| 120 |
> |
} |
| 121 |
> |
|
| 122 |
> |
RealType SCDElem::calcSCD(Snapshot* snapshot) { |
| 123 |
> |
std::vector<SDTuple3>::iterator i; |
| 124 |
> |
Vector3d normal(0.0, 0.0, 1.0); |
| 125 |
> |
RealType scd = 0.0; |
| 126 |
> |
for (i = tuples_.begin(); i != tuples_.end(); ++i) { |
| 127 |
> |
//Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988 |
| 128 |
> |
|
| 129 |
> |
Vector3d zAxis = i->third->getPos() - i->first->getPos(); |
| 130 |
> |
if (usePeriodicBoundaryConditions_) |
| 131 |
> |
snapshot->wrapVector(zAxis); |
| 132 |
> |
Vector3d v12 = i->second->getPos() - i->first->getPos(); |
| 133 |
> |
if (usePeriodicBoundaryConditions_) |
| 134 |
> |
snapshot->wrapVector(v12); |
| 135 |
> |
Vector3d xAxis = cross(v12, zAxis); |
| 136 |
> |
Vector3d yAxis = cross(zAxis, xAxis); |
| 137 |
> |
|
| 138 |
> |
xAxis.normalize(); |
| 139 |
> |
yAxis.normalize(); |
| 140 |
> |
zAxis.normalize(); |
| 141 |
> |
RealType cosThetaX = dot(xAxis, normal); |
| 142 |
> |
RealType sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0); |
| 143 |
> |
RealType cosThetaY = dot(yAxis, normal); |
| 144 |
> |
RealType syy = 0.5*(3*cosThetaY * cosThetaY - 1.0); |
| 145 |
> |
scd += 2.0/3.0*sxx + 1.0/3.0*syy; |
| 146 |
> |
} |
| 147 |
> |
scd /= tuples_.size(); |
| 148 |
> |
return scd; |
| 149 |
> |
|
| 150 |
> |
} |
| 151 |
> |
|
| 152 |
> |
SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename, |
| 153 |
> |
const std::string& sele1, const std::string& sele2, const std::string& sele3) |
| 154 |
> |
: StaticAnalyser(info, filename) { |
| 155 |
> |
|
| 156 |
> |
setOutputName(getPrefix(filename) + ".scd"); |
| 157 |
> |
|
| 158 |
> |
scdElems_.push_back(SCDElem(info, sele1, sele2, sele3)); |
| 159 |
> |
scdParam_.resize(scdElems_.size()); |
| 160 |
> |
std::fill(scdParam_.begin(), scdParam_.end(), 0.0); |
| 161 |
> |
|
| 162 |
> |
} |
| 163 |
> |
|
| 164 |
> |
SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename, |
| 165 |
> |
const std::string& molname, int beginIndex, int endIndex) |
| 166 |
> |
: StaticAnalyser(info, filename) { |
| 167 |
> |
|
| 168 |
> |
setOutputName(getPrefix(filename) + ".scd"); |
| 169 |
> |
|
| 170 |
> |
assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2); |
| 171 |
> |
for (int i = beginIndex; i <= endIndex -2 ; ++i) { |
| 172 |
> |
std::string selectionTemplate = "select " + molname + "."; |
| 173 |
> |
std::string sele1 = selectionTemplate + OpenMD_itoa(i); |
| 174 |
> |
std::string sele2 = selectionTemplate + OpenMD_itoa(i+1); |
| 175 |
> |
std::string sele3 = selectionTemplate + OpenMD_itoa(i+2); |
| 176 |
> |
|
| 177 |
> |
scdElems_.push_back(SCDElem(info, sele1, sele2, sele3)); |
| 178 |
> |
} |
| 179 |
> |
|
| 180 |
> |
scdParam_.resize(scdElems_.size()); |
| 181 |
> |
std::fill(scdParam_.begin(), scdParam_.end(), 0.0); |
| 182 |
> |
} |
| 183 |
> |
|
| 184 |
> |
|
| 185 |
> |
void SCDOrderParameter::process() { |
| 186 |
> |
Molecule* mol; |
| 187 |
> |
RigidBody* rb; |
| 188 |
> |
SimInfo::MoleculeIterator mi; |
| 189 |
> |
Molecule::RigidBodyIterator rbIter; |
| 190 |
> |
|
| 191 |
> |
DumpReader reader(info_, dumpFilename_); |
| 192 |
> |
int nFrames = reader.getNFrames(); |
| 193 |
> |
|
| 194 |
> |
for (int i = 0; i < nFrames; i += step_) { |
| 195 |
> |
reader.readFrame(i); |
| 196 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 197 |
> |
|
| 198 |
> |
|
| 199 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 200 |
> |
//change the positions of atoms which belong to the rigidbodies |
| 201 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 202 |
> |
rb->updateAtoms(); |
| 203 |
> |
} |
| 204 |
> |
|
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
for (std::size_t j = 0; j < scdElems_.size(); ++j) { |
| 208 |
> |
scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_); |
| 209 |
> |
} |
| 210 |
> |
|
| 211 |
> |
} |
| 212 |
> |
|
| 213 |
> |
int nProcessed = nFrames /step_; |
| 214 |
> |
for (std::size_t j = 0; j < scdElems_.size(); ++j) { |
| 215 |
> |
scdParam_[j] /= nProcessed; |
| 216 |
> |
} |
| 217 |
> |
|
| 218 |
> |
writeSCD(); |
| 219 |
> |
|
| 220 |
> |
} |
| 221 |
> |
|
| 222 |
> |
void SCDOrderParameter::writeSCD() { |
| 223 |
> |
|
| 224 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 225 |
> |
os << "#scd parameter\n"; |
| 226 |
> |
for (std::size_t i = 0; i < scdElems_.size(); ++i) { |
| 227 |
> |
os << "#[column " << i+1 << "]\t" |
| 228 |
> |
<< "sele1: \"" << scdElems_[i].getSelection1() << "\",\t" |
| 229 |
> |
<< "sele2: \"" << scdElems_[i].getSelection2() << "\",\t" |
| 230 |
> |
<< "sele3: \"" << scdElems_[i].getSelection3() << "\"\n"; |
| 231 |
> |
} |
| 232 |
> |
|
| 233 |
> |
for (std::size_t i = 0; i < scdElems_.size(); ++i) { |
| 234 |
> |
os << scdParam_[i]<< "\t"; |
| 235 |
> |
} |
| 236 |
> |
os << std::endl; |
| 237 |
> |
} |
| 238 |
> |
|
| 239 |
> |
|
| 240 |
> |
} |
| 241 |
> |
|
| 242 |
> |
|
