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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/RippleOP.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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namespace OpenMD { |
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|
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|
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RippleOP::RippleOP(SimInfo* info, const std::string& filename, |
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const std::string& sele1, const std::string& sele2) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), |
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seleMan1_(info), seleMan2_(info), evaluator1_(info), evaluator2_(info) { |
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|
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setOutputName(getPrefix(filename) + ".rp2"); |
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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 = 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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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 = 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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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 = 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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|
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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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void RippleOP::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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StuntDouble* j1; |
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StuntDouble* j2; |
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StuntDouble* sd3; |
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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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int nMolecules = info_->getNGlobalMolecules(); |
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int i1; |
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int nUpper=0; |
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int nLower=0; |
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int nTail=0; |
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RealType sumZ = 0.0; |
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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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for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; |
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sd3 = seleMan2_.nextSelected(i1)) { |
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Vector3d pos1 = sd3->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(pos1); |
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sd3->setPos(pos1); |
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} |
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|
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for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; |
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sd3 = seleMan2_.nextSelected(i1)) { |
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Vector3d pos1 = sd3->getPos(); |
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sumZ += pos1.z(); |
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} |
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RealType avgZ = sumZ / (RealType) nMolecules; |
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|
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Mat3x3d orderTensorHeadUpper(0.0); |
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Mat3x3d orderTensorTail(0.0); |
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Mat3x3d orderTensorHeadLower(0.0); |
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for (j1 = seleMan1_.beginSelected(i1); j1 != NULL; |
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j1 = seleMan1_.nextSelected(i1)) { |
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Vector3d pos = j1->getPos(); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(pos); |
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Vector3d vecHeadUpper; |
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if (pos.z() >= avgZ){ |
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AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType(); |
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MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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if (ma1.isDipole()) |
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vecHeadUpper = j1->getDipole(); |
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else |
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vecHeadUpper = j1->getA().transpose()*V3Z; |
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nUpper++; |
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} |
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Vector3d vecHeadLower; |
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if (pos.z() <= avgZ){ |
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AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType(); |
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MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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if (ma1.isDipole()) |
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vecHeadLower = j1->getDipole(); |
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else |
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vecHeadLower = j1->getA().transpose() * V3Z; |
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nLower++; |
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} |
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orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper); |
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orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower); |
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} |
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for (j2 = seleMan2_.beginSelected(i1); j2 != NULL; |
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j2 = seleMan2_.nextSelected(i1)) { |
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// The lab frame vector corresponding to the body-fixed |
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// z-axis is simply the second column of A.transpose() |
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// or, identically, the second row of A itself. |
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|
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Vector3d vecTail = j2->getA().getRow(2); |
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orderTensorTail +=outProduct(vecTail, vecTail); |
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nTail++; |
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} |
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|
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orderTensorHeadUpper /= (RealType) nUpper; |
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orderTensorHeadLower /= (RealType) nLower; |
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orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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|
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orderTensorTail /= (RealType) nTail; |
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orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
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|
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Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail; |
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Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail; |
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Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper, |
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eigenvectorsHeadUpper); |
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Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower, |
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eigenvectorsHeadLower); |
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Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail); |
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|
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int whichUpper(-1), whichLower(-1), whichTail(-1); |
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RealType maxEvalUpper = 0.0; |
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RealType maxEvalLower = 0.0; |
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RealType maxEvalTail = 0.0; |
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for(int k = 0; k< 3; k++){ |
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if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){ |
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whichUpper = k; |
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maxEvalUpper = fabs(eigenvaluesHeadUpper[k]); |
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} |
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} |
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RealType p2HeadUpper = 1.5 * maxEvalUpper; |
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for(int k = 0; k< 3; k++){ |
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if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){ |
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whichLower = k; |
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maxEvalLower = fabs(eigenvaluesHeadLower[k]); |
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} |
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} |
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RealType p2HeadLower = 1.5 * maxEvalLower; |
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for(int k = 0; k< 3; k++){ |
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if(fabs(eigenvaluesTail[k]) > maxEvalTail){ |
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whichTail = k; |
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maxEvalTail = fabs(eigenvaluesTail[k]); |
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} |
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} |
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RealType p2Tail = 1.5 * maxEvalTail; |
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|
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//the eigenvector is already normalized in SquareMatrix3::diagonalize |
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Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper); |
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if (directorHeadUpper[0] < 0) { |
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directorHeadUpper.negate(); |
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} |
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Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower); |
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if (directorHeadLower[0] < 0) { |
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directorHeadLower.negate(); |
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} |
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Vector3d directorTail = eigenvectorsTail.getColumn(whichTail); |
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if (directorTail[0] < 0) { |
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directorTail.negate(); |
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} |
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|
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OrderParam paramHeadUpper, paramHeadLower, paramTail; |
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paramHeadUpper.p2 = p2HeadUpper; |
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paramHeadUpper.director = directorHeadUpper; |
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paramHeadLower.p2 = p2HeadLower; |
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paramHeadLower.director = directorHeadLower; |
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paramTail.p2 = p2Tail; |
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paramTail.director = directorTail; |
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|
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orderParamsHeadUpper_.push_back(paramHeadUpper); |
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orderParamsHeadLower_.push_back(paramHeadLower); |
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orderParamsTail_.push_back(paramTail); |
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|
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} |
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|
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OrderParam sumOPHeadUpper, errsumOPHeadUpper; |
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OrderParam sumOPHeadLower, errsumOPHeadLower; |
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OrderParam sumOPTail, errsumOPTail; |
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|
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sumOPHeadUpper.p2 = 0.0; |
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errsumOPHeadUpper.p2 = 0.0; |
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sumOPHeadLower.p2 = 0.0; |
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errsumOPHeadLower.p2 = 0.0; |
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for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
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sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2; |
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sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0]; |
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sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1]; |
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sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2]; |
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} |
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|
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avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size(); |
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avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size(); |
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avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size(); |
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avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size(); |
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for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
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errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2); |
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} |
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errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size()); |
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for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
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sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2; |
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sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0]; |
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sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1]; |
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sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2]; |
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} |
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|
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avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size(); |
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avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size(); |
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avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size(); |
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avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size(); |
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for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
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errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2); |
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} |
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errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size()); |
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|
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sumOPTail.p2 = 0.0; |
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errsumOPTail.p2 = 0.0; |
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for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) { |
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sumOPTail.p2 += orderParamsTail_[i].p2; |
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sumOPTail.director[0] += orderParamsTail_[i].director[0]; |
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sumOPTail.director[1] += orderParamsTail_[i].director[1]; |
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sumOPTail.director[2] += orderParamsTail_[i].director[2]; |
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} |
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|
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avgOPTail.p2 = sumOPTail.p2 / (RealType)orderParamsTail_.size(); |
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avgOPTail.director[0] = sumOPTail.director[0] / (RealType)orderParamsTail_.size(); |
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avgOPTail.director[1] = sumOPTail.director[1] / (RealType)orderParamsTail_.size(); |
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avgOPTail.director[2] = sumOPTail.director[2] / (RealType)orderParamsTail_.size(); |
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for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) { |
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errsumOPTail.p2 += pow((orderParamsTail_[i].p2 - avgOPTail.p2), 2); |
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} |
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errOPTail.p2 = sqrt(errsumOPTail.p2 / (RealType)orderParamsTail_.size()); |
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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 RippleOP::writeP2() { |
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|
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std::ofstream os(getOutputFileName().c_str()); |
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os<< "#selection1: (" << selectionScript1_ << ")\n"; |
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os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |
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|
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os << avgOPHeadUpper.p2 << "\t" |
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<< errOPHeadUpper.p2 << "\t" |
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<< avgOPHeadUpper.director[0] << "\t" |
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<< avgOPHeadUpper.director[1] << "\t" |
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<< avgOPHeadUpper.director[2] << "\n"; |
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|
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os << avgOPHeadLower.p2 << "\t" |
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<< errOPHeadLower.p2 << "\t" |
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<< avgOPHeadLower.director[0] << "\t" |
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<< avgOPHeadLower.director[1] << "\t" |
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<< avgOPHeadLower.director[2] << "\n"; |
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|
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |
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|
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os << avgOPTail.p2 << "\t" |
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<< errOPTail.p2 << "\t" |
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<< avgOPTail.director[0] << "\t" |
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<< avgOPTail.director[1] << "\t" |
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<< avgOPTail.director[2] << "\n"; |
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} |
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|
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} |
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|
