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/* |
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* sphericalNanoparticle.cpp |
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* OOPSE-2.0 |
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* |
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* Created by Charles F. Vardeman II on 9/28/05. |
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* Copyright 2005 __MyCompanyName__. All rights reserved. |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "sphericalNanoparticle.hpp" |
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <cmath> |
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#include <iostream> |
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#include <string> |
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#include <map> |
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#include <fstream> |
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|
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#include "config.h" |
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|
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|
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#include "lattice/LatticeFactory.hpp" |
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#include "utils/MoLocator.hpp" |
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#include "lattice/Lattice.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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using namespace oopse; |
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|
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sphericalNanoparticle::sphericalNanoparticle(double radius, int latticeCnst){ |
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|
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particleRadius = radius; |
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particleDiameter = 2.0 * radius; |
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latticeConstant = latticeCnst; |
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|
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// Number of Unit Cells in Length first |
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ny_ = (int)(particleDiameter/latticeConstant); |
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// Number of unit cells in Width |
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nx_ = (int)(particleDiameter/latticeConstant); |
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nz_ = (int)(particleDiameter/latticeConstant); |
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} |
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|
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int sphericalNanoparticle::getNMol(Lattice& simpleLat){ |
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int numMol; |
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int numMolPerCell |
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std::vector<Vector3d> latticePos; |
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|
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numMol = 0; |
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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for(int i = -nx_; i < nx_; i++) { |
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for(int j = -ny_; j < ny_; j++) { |
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for(int k = -nz_; k < nz_; k++) { |
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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|
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for(int l = 0; l < numMolPerCell; l++) { |
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rx = latticePos[l][0]; |
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ry = latticePos[l][1]; |
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rz = latticePos[l][2]; |
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dist = sqrt(rx*rx + ry*ry + rz*rz) |
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if (dist <= particleRadius){ |
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numMol++; |
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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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return numMol; |
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} |
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|
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int sphericalNanoparticle::getNMol(Lattice &simpleLat, int nComponents, double &shellRadius,int &numSites){ |
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int numMol; |
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int numMolPerCell |
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std::vector<Vector3d> latticePos; |
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|
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numMol = 0; |
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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for(int i = -nx_; i < nx_; i++) { |
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for(int j = -ny_; j < ny_; j++) { |
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for(int k = -nz_; k < nz_; k++) { |
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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|
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for(int l = 0; l < numMolPerCell; l++) { |
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rx = latticePos[l][0]; |
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ry = latticePos[l][1]; |
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rz = latticePos[l][2]; |
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dist = sqrt(rx*rx + ry*ry + rz*rz) |
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if (dist <= particleRadius){ |
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for (int l = 0; l< nComponents -1;l++){ |
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if (dist <= shellRadius[l]{ |
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numMol++; |
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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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|
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return numMol; |
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} |
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void sphericalNanoparticle::buildSphericalNanoparticle(Molecule* ){ |
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} |
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