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/* |
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* Copyright (c) 2006 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] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by Kelsey M. Stocker on 2/9/12. |
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* @author Kelsey M. Stocker |
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* @version $Id: shapedLatticeRod.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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#include "lattice/shapedLattice.hpp" |
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#include "shapedLatticePentRod.hpp" |
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#include "shapedLatticeRod.hpp" |
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#include <cmath> |
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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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shapedLatticePentRod::shapedLatticePentRod(RealType latticeConstant, |
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std::string latticeType, |
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RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){ |
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|
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rodRadius_= radius; |
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rodLength_= length; |
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Vector3d dimension; |
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dimension[0] = 2.0*length; |
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dimension[1] = 2.0*length; |
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dimension[2] = 2.0*length; |
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cerr << "using dimension = " << dimension << "\n"; |
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setGridDimension(dimension); |
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cerr << "done!\n"; |
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Vector3d origin; |
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origin[0] = 0; |
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origin[1] = 0; |
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origin[2] = 2.04; |
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setOrigin(origin); |
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} |
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|
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|
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/** |
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* Creates a wedge for pentagonal nanorods |
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* |
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*/ |
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|
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bool shapedLatticePentRod::isInterior(Vector3d point){ |
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|
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RealType x, y, z, new_x, new_y, left_newx, right_newx; |
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// int z_int; |
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|
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bool isIT=false; |
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|
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x = point[0]; |
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y = point[1]; |
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z = point[2]; |
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|
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// z_int = int(z/2.04); |
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|
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//Rotate by 45 degrees around z-axis so length of rod lies along y axis |
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new_x = (sqrt(2.0)/2)*(x - y); |
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new_y = (sqrt(2.0)/2)*(x + y); |
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|
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left_newx = (z - 1.44)*(0.577350269/0.816496581); |
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right_newx = (z + 1.44)*(-0.577350269/0.816496581); |
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|
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//Make center spine of nanorod down new_y axis |
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//This is now done directly in nanorod_pentBuilder.cpp |
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/*if ( (new_x == 0) && (z == 0) ) { |
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|
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if ( abs(new_y) <= 0.5*rodLength_ + 0.5773502692*rodRadius_ ) { |
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|
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isIT = true; |
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|
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} |
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}*/ |
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|
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//Make one wedge |
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if ( (z < 0) && (z >= -0.816496581*rodRadius_ - 1.44) ) { |
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|
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if ( abs(new_y) <= 1.44*(z/2.04) + 0.5*rodLength_ + 0.5773502692*rodRadius_ ) { |
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|
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if ( (new_x >= left_newx) && (new_x <= right_newx) ) { |
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|
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isIT=true; |
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|
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} |
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} |
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} |
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return isIT; |
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} |
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} |
