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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "applications/staticProps/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, |
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const std::string& sele2, const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){ |
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|
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usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions(); |
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|
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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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RealType 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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RealType scd = 0.0; |
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for (i = tuples_.begin(); i != tuples_.end(); ++i) { |
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//Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988 |
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|
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Vector3d zAxis = i->third->getPos() - i->first->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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snapshot->wrapVector(zAxis); |
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Vector3d v12 = i->second->getPos() - i->first->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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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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RealType cosThetaX = dot(xAxis, normal); |
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RealType sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0); |
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RealType cosThetaY = dot(yAxis, normal); |
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RealType 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" |
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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) { |
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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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|
