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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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|
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using namespace std; |
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namespace OpenMD { |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1) |
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: StaticAnalyser(info, filename), doVect_(true), doOffset_(false), |
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selectionScript1_(sele1), evaluator1_(info), |
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evaluator2_(info), 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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} |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1, const string& sele2) |
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: StaticAnalyser(info, filename), doVect_(false), doOffset_(false), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
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evaluator2_(info), 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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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1, int seleOffset) |
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: StaticAnalyser(info, filename), doVect_(false), doOffset_(true), |
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seleOffset_(seleOffset), selectionScript1_(sele1), evaluator1_(info), |
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evaluator2_(info), 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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} |
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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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StuntDouble* sd1; |
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StuntDouble* sd2; |
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int ii; |
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int jj; |
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int vecCount; |
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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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for (mol = info_->beginMolecule(mi); mol != NULL; |
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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; |
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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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Mat3x3d orderTensor(0.0); |
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vecCount = 0; |
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|
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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|
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if (doVect_) { |
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|
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for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(ii)) { |
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if (sd1->isDirectional()) { |
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Vector3d vec = sd1->getA().getColumn(2); |
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vec.normalize(); |
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orderTensor += outProduct(vec, vec); |
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vecCount++; |
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} |
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} |
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|
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orderTensor /= vecCount; |
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|
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} else { |
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|
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if (doOffset_) { |
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|
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for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(ii)) { |
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|
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// This will require careful rewriting if StaticProps is |
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// ever parallelized. For an example, see |
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// Thermo::getTaggedAtomPairDistance |
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|
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int sd2Index = sd1->getGlobalIndex() + seleOffset_; |
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sd2 = info_->getIOIndexToIntegrableObject(sd2Index); |
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|
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Vector3d vec = sd1->getPos() - sd2->getPos(); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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vec.normalize(); |
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|
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orderTensor +=outProduct(vec, vec); |
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vecCount++; |
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} |
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|
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orderTensor /= vecCount; |
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} else { |
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|
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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|
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if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
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sprintf( painCave.errMsg, |
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"In frame %d, the number of selected StuntDoubles are\n" |
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"\tnot the same in --sele1 and sele2\n", i); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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for (sd1 = seleMan1_.beginSelected(ii), |
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sd2 = seleMan2_.beginSelected(jj); |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(ii), |
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sd2 = seleMan2_.nextSelected(jj)) { |
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|
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Vector3d vec = sd1->getPos() - sd2->getPos(); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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vec.normalize(); |
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|
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orderTensor +=outProduct(vec, vec); |
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vecCount++; |
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} |
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|
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orderTensor /= vecCount; |
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} |
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} |
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|
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if (vecCount == 0) { |
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sprintf( painCave.errMsg, |
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"In frame %d, the number of selected vectors was zero.\n" |
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"\tThis will not give a meaningful order parameter.", i); |
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painCave.severity = OPENMD_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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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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|
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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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vecCount = 0; |
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|
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if (doVect_) { |
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for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(ii)) { |
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if (sd1->isDirectional()) { |
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Vector3d vec = sd1->getA().getColumn(2); |
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vec.normalize(); |
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angle += acos(dot(vec, director)); |
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vecCount++; |
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} |
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} |
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angle = angle/(vecCount*NumericConstant::PI)*180.0; |
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|
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} else { |
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if (doOffset_) { |
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|
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for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(ii)) { |
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|
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// This will require careful rewriting if StaticProps is |
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// ever parallelized. For an example, see |
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// Thermo::getTaggedAtomPairDistance |
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|
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int sd2Index = sd1->getGlobalIndex() + seleOffset_; |
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sd2 = info_->getIOIndexToIntegrableObject(sd2Index); |
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|
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Vector3d vec = sd1->getPos() - sd2->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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angle += acos(dot(vec, director)) ; |
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vecCount++; |
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} |
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angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
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|
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} else { |
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|
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for (sd1 = seleMan1_.beginSelected(ii), |
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sd2 = seleMan2_.beginSelected(jj); |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(ii), |
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sd2 = seleMan2_.nextSelected(jj)) { |
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|
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Vector3d vec = sd1->getPos() - sd2->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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vec.normalize(); |
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angle += acos(dot(vec, director)) ; |
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vecCount++; |
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} |
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angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
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} |
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} |
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|
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OrderParam param; |
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param.p2 = p2; |
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param.director = director; |
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param.angle = angle; |
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|
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orderParams_.push_back(param); |
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|
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} |
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|
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writeP2(); |
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|
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} |
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|
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void P2OrderParameter::writeP2() { |
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|
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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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if (!doVect_) { |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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} |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
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|
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for (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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|
