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/* Copyright (c) 2006, 2009, 2010 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, 24107 (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/NanoLength.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 OpenMD; |
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|
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bool pairComparator( const evIndex& l, const evIndex& r) { |
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return l.first < r.first; |
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} |
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|
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NanoLength::NanoLength(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) { |
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setOutputName(getPrefix(filename) + ".length"); |
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|
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osq.open(getOutputFileName().c_str()); |
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|
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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frameCounter_ = 0; |
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} |
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|
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void NanoLength::process() { |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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Vector3d vec; |
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int i,j; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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|
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theAtoms_.reserve(info_->getNGlobalAtoms()); |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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RealType time = currentSnapshot_->getTime(); |
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|
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// Clear pos vector between each frame. |
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theAtoms_.clear(); |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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// update the positions of atoms which belong to the rigidbodies |
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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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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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// outer loop is over the selected StuntDoubles: |
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|
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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theAtoms_.push_back(sd); |
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} |
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|
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RealType rodLength = getLength(theAtoms_); |
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|
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osq.precision(7); |
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if (osq.is_open()){ |
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osq << time << "\t" << rodLength << std::endl; |
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} |
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} |
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} |
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|
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RealType NanoLength::getLength(std::vector<StuntDouble*> atoms) { |
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Vector3d COM(0.0); |
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RealType mass = 0.0; |
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RealType mtmp; |
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for (std::vector<StuntDouble*>::iterator i = atoms.begin(); |
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i != atoms.end(); ++i) { |
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mtmp = (*i)->getMass(); |
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mass += mtmp; |
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COM += (*i)->getPos() * mtmp; |
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} |
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COM /= mass; |
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|
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// Moment of Inertia calculation |
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Mat3x3d Itmp(0.0); |
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for (std::vector<StuntDouble*>::iterator i = atoms.begin(); |
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i != atoms.end(); ++i) { |
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|
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Mat3x3d IAtom(0.0); |
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mtmp = (*i)->getMass(); |
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Vector3d delta = (*i)->getPos() - COM; |
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IAtom -= outProduct(delta, delta) * mtmp; |
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RealType r2 = delta.lengthSquare(); |
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IAtom(0, 0) += mtmp * r2; |
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IAtom(1, 1) += mtmp * r2; |
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IAtom(2, 2) += mtmp * r2; |
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Itmp += IAtom; |
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} |
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|
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//diagonalize |
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Vector3d evals; |
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Mat3x3d evects; |
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Mat3x3d::diagonalize(Itmp, evals, evects); |
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|
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// we need to re-order the axes so that the smallest moment of |
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// inertia (which corresponds to the long axis of the rod) is |
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// along the z-axis. We'll just reverse the order of the three |
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// axes. Python has an argsort function, but we had to invent our |
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// own: |
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|
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std::vector<evIndex> evals_prime; |
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for (int i = 0; i < 3; i++) |
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evals_prime.push_back(std::make_pair(evals[i], i)); |
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std::sort(evals_prime.begin(), evals_prime.end(), pairComparator); |
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|
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RotMat3x3d A; |
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Mat3x3d I; |
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|
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for (int i = 0; i < 3; i++) { |
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int index = evals_prime[2-i].second; |
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A.setColumn(i, evects.getColumn(index)); |
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I(i,i) = evals[index]; |
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} |
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|
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// now project the delta from the center of mass onto the long |
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// axis of the object |
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|
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Vector3d longAxis = A.getColumn(2); |
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RealType axisLength = longAxis.length(); |
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RealType projmin = 0.0; |
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RealType projmax = 0.0; |
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|
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for (std::vector<StuntDouble*>::iterator i = atoms.begin(); |
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i != atoms.end(); ++i) { |
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Vector3d delta = (*i)->getPos() - COM; |
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RealType projection = dot(delta, longAxis) / axisLength; |
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if (projection > projmax) projmax = projection; |
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if (projection < projmin) projmin = projection; |
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} |
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|
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return projmax - projmin; |
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} |
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|
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|
