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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, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by Joseph R. Michalka on Oct 12 2012 |
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* @author Joseph R. Michalka |
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* @version $Id: RhoZ.cpp 1665 2011-11-22 20:38:56Z gezelter $ |
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* |
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*/ |
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|
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/* Surface Diffusion |
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* Attempting to track/measure the surface diffusion rates of particles on... wait for it.. |
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* a surface. |
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* This program was initially created to track Platinum particles moving around a 557 surface. |
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* Hence why we are trying to keep the x and y movement separate. |
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* |
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*/ |
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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/SurfaceDiffusion.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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namespace OpenMD { |
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|
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SurfaceDiffusion::SurfaceDiffusion(SimInfo* info, const std::string& filename, const std::string& sele, RealType len) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan1_(info){ |
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|
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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//Depending on the selection 'sele1="select Pt"' need a vector equal to the |
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//number of Platinums in the system (for this specific case) |
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selectionCount_ = seleMan1_.getSelectionCount(); |
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cout << "SelectionCount_: " << selectionCount_ << "\n"; |
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|
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moBool_.resize(selectionCount_); |
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positions_.resize(selectionCount_); |
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|
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filename_ = filename; |
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singleMoveDistance_ = 2.0; |
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} |
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|
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SurfaceDiffusion::~SurfaceDiffusion(){ |
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|
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} |
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|
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void SurfaceDiffusion::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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StuntDouble* sd; |
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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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frames_ = 0; |
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nProcessed_ = nFrames/step_; |
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|
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//positions_ and moBool_ are 2D arrays, need the second dimension filled as well |
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for(int i = 0; i < selectionCount_; i++){ |
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moBool_[i].resize(nFrames); |
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positions_[i].resize(nFrames); |
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} |
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|
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int iterator; |
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int index = 0; |
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/* Loop over all frames storing the positions in a vec< vec<pos> > |
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* At the end, positions.length() should equal seleMan1_.size() or w/e |
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* And positions[index].length() should equal nFrames (or nFrames/istep) |
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*/ |
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for(int istep = 0; istep < nFrames; istep += step_){ |
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frames_++; |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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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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index = 0; //count over atoms since iterators aren't the most friendly for such plebian things |
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for(sd = seleMan1_.beginSelected(iterator); sd != NULL; sd = seleMan1_.nextSelected(iterator)){ |
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Vector3d pos = sd->getPos(); |
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positions_[index][istep] = pos; |
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index++; |
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} |
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} |
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|
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|
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cout << "Position Array size: " << positions_.size() << "\n"; |
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cout << "Frames analyzed: " << positions_[0].size() << "\n"; |
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|
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|
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for(int i = 0; i < positions_.size(); i++){ |
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int frameIndex = positions_[i].size(); |
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for(int j = 1; j < frameIndex; j++){ |
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Vector3d posF1 = positions_[i][j-1]; |
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Vector3d posF2 = positions_[i][j]; |
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Vector3d diff = posF2 - posF1; |
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if(usePeriodicBoundaryConditions_){ |
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currentSnapshot_->wrapVector(diff); |
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} |
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double dist = diff.length(); |
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if(dist > singleMoveDistance_){ |
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moBool_[i][j] = true; |
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}else{ |
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moBool_[i][j] = false; |
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} |
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} |
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} |
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|
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int mobileAtomCount = 0; |
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for(int i = 0; i < moBool_.size(); i++){ |
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int frameIndex = moBool_[i].size(); |
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bool mobileAtom = false; |
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for(int j = 0; j < frameIndex; j++){ |
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mobileAtom = mobileAtom || moBool_[i][j]; |
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} |
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moBool_[i][0] = mobileAtom; //is true if any value later in the array is true, false otherwise |
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if(mobileAtom){ |
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mobileAtomCount++; |
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} |
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} |
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|
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cout << "Mobile atom count: " << mobileAtomCount << "\n"; |
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|
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//Here I shrink the size of the arrays, why look through 3888, when you only need ~800. |
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//Additionally, all of these are mobile at some point in time, the others aren't, dead weight and |
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//memory |
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positions2_.resize(mobileAtomCount); |
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moBool2_.resize(mobileAtomCount); |
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int pos2index = 0; |
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for(int i = 0; i < positions_.size(); i++){ |
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int frameCount = positions_[i].size(); |
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if(moBool_[i][0]){ |
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for(int j = 0; j < frameCount; j++){ |
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positions2_[pos2index].push_back(positions_[i][j]); |
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moBool2_[pos2index].push_back(moBool_[i][j]); |
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} |
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pos2index++; |
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} |
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} |
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|
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positions_.clear(); |
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moBool_.clear(); |
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|
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cout << "positions_ has been cleared: " << positions_.size() << "\n"; |
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cout << "positions2_ has been filled: " << positions2_.size() << "\n"; |
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cout << "positions2_ has " << positions2_[0].size() << " frames\n"; |
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|
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//The important one! |
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positionCorrelation(); |
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|
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|
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//Write out my data |
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std::ofstream diffStream; |
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setOutputName(getPrefix(filename_) + ".Mdiffusion"); |
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diffStream.open(outputFilename_.c_str()); |
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diffStream << "#X&Y diffusion amounts\n"; |
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diffStream << "#singleMoveDistance_: " << singleMoveDistance_ << "\n"; |
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|
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diffStream << "#Number of mobile atoms: " << positions2_.size() << "\n"; |
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|
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diffStream << "#time, <x(t)-x(0)>, <y(t)-y(0)>, <r(t)-r(0)>\n"; |
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for(int i = 0; i < xHist_.size(); i++){ |
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diffStream << i << ", " << xHist_[i] << ", " << yHist_[i] << ", " << rHist_[i] << "\n"; |
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} |
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diffStream.close(); |
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|
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} |
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|
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void SurfaceDiffusion::positionCorrelation(){ |
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RealType xDist = 0.0; |
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RealType yDist = 0.0; |
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RealType rDist = 0.0; |
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int timeShift = 0; |
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Vector3d kPos; |
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Vector3d jPos; |
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//biggest timeShift is positions2_[0].size() - 1? |
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xHist_.clear(); |
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yHist_.clear(); |
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rHist_.clear(); |
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count_.clear(); |
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int frameResize = positions2_[0].size(); |
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xHist_.resize(frameResize); |
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yHist_.resize(frameResize); |
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rHist_.resize(frameResize); |
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count_.resize(frameResize); |
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//loop over particles |
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// loop over frames starting at j |
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// loop over frames starting at k = j (time shift of 0) |
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for(int i = 0; i < positions2_.size(); i++){ |
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int frames = positions2_[i].size() - 1; //for counting properly, otherwise moBool2_[i][j+1] will |
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// go over |
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for(int j = 0; j < frames; j++){ |
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//if the particle is mobile between j and j + 1, then count it for all timeShifts |
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if(moBool2_[i][j+1]){ |
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for(int k = j; k < positions2_[0].size(); k++){ |
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//<x(t)-x(0)> <y(t)-y(0)> <r(t)-r(0)> |
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//The positions stored are not wrapped, thus I don't need to worry about pbc |
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//Mean square displacement |
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//So I do want the squared distances |
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|
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kPos = positions2_[i][k]; |
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jPos = positions2_[i][j]; |
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xDist = kPos.x() - jPos.x(); |
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xDist = xDist*xDist; |
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|
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yDist = kPos.y() - jPos.y(); |
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yDist = yDist*yDist; |
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|
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rDist = (kPos - jPos).lengthSquare(); |
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|
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|
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timeShift = k - j; |
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xHist_[timeShift] += xDist; |
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yHist_[timeShift] += yDist; |
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rHist_[timeShift] += rDist; |
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count_[timeShift]++; |
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} |
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} |
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} |
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} |
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cout << "X, Y, R calculated\n"; |
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|
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for(int i = 0; i < xHist_.size(); i++){ |
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xHist_[i] = xHist_[i]/(count_[i]); |
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yHist_[i] = yHist_[i]/(count_[i]); |
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rHist_[i] = rHist_[i]/(count_[i]); |
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} |
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cout << "X, Y, R normalized\n"; |
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} |
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|
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} |
