applications/nanoparticleBuilder/shapedLatticeRod.cpp

/*
 * Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by Kelsey M. Stocker on 2/9/12.
 *  @author  Kelsey M. Stocker 
 *  @version $Id: shapedLatticeRod.cpp 1665 2011-11-22 20:38:56Z gezelter $
 *
 */

#include "lattice/shapedLattice.hpp"
#include "shapedLatticeRod.hpp"
#include <cmath>

using namespace std;
namespace OpenMD {
  
  shapedLatticeRod::shapedLatticeRod(RealType latticeConstant,
                                     std::string latticeType, 
                                     RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){
    
    rodRadius_= radius;
    rodLength_= length;
    RealType x, y, z, distance, delta_z;
    Vector3d dimension;
    dimension[0] = 3.0*radius;
    dimension[1] = 3.0*radius;
    dimension[2] = length + 3.0*radius;
    cerr << "using dimension = " << dimension << "\n";
    setGridDimension(dimension);
    cerr << "done!\n";
    Vector3d origin;
    origin[0] = 0;
    origin[1] = 0;
    origin[2] = 0;
    setOrigin(origin);
  }


  /**
   * Determines whether a point lies within a spherically-capped nanorod at origin (0,0,0)
   *
   */ 

  bool shapedLatticeRod::isInterior(Vector3d point){

    RealType x, y, z, distance, delta_z;

    distance = 0;
    
    x = point[0];
    y = point[1];
    z = point[2];
    //  std::cerr << "Testing xyz = " << point << " \n";
    
    if ( abs(z) >= rodLength_/2.0 ) {
      delta_z = abs(z) - rodLength_/2.0;
      distance = sqrt((x*x) + (y*y) + (delta_z*delta_z));
      //    std::cerr << "abs_end " ;
    } else {
      distance = sqrt((x*x) + (y*y)); 
      //   std::cerr << "middle ";
    }
    
    bool isIT=false;
    if ( distance <= rodRadius_ ) {
      //   cerr << "accepted!\n";
      isIT=true;
    } else {
      //     cerr << "rejected!\n";
    }
    return isIT;
  }
    
}
Revision:	1701
Committed:	Thu Apr 5 19:37:58 2012 UTC (13 years, 1 month ago) by kstocke1
File size:	3904 byte(s)
Log Message:	Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
#	User	Rev	Content
1	kstocke1	1701	/*
2			* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41			* Created by Kelsey M. Stocker on 2/9/12.
42			* @author Kelsey M. Stocker
43			* @version $Id: shapedLatticeRod.cpp 1665 2011-11-22 20:38:56Z gezelter $
44			*
45			*/
46
47			#include "lattice/shapedLattice.hpp"
48			#include "shapedLatticeRod.hpp"
49			#include <cmath>
50
51			using namespace std;
52			namespace OpenMD {
53
54			shapedLatticeRod::shapedLatticeRod(RealType latticeConstant,
55			std::string latticeType,
56			RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){
57
58			rodRadius_= radius;
59			rodLength_= length;
60			RealType x, y, z, distance, delta_z;
61			Vector3d dimension;
62			dimension[0] = 3.0*radius;
63			dimension[1] = 3.0*radius;
64			dimension[2] = length + 3.0*radius;
65			cerr << "using dimension = " << dimension << "\n";
66			setGridDimension(dimension);
67			cerr << "done!\n";
68			Vector3d origin;
69			origin[0] = 0;
70			origin[1] = 0;
71			origin[2] = 0;
72			setOrigin(origin);
73			}
74
75
76			/**
77			* Determines whether a point lies within a spherically-capped nanorod at origin (0,0,0)
78			*
79			*/
80
81			bool shapedLatticeRod::isInterior(Vector3d point){
82
83			RealType x, y, z, distance, delta_z;
84
85			distance = 0;
86
87			x = point[0];
88			y = point[1];
89			z = point[2];
90			// std::cerr << "Testing xyz = " << point << " \n";
91
92			if ( abs(z) >= rodLength_/2.0 ) {
93			delta_z = abs(z) - rodLength_/2.0;
94			distance = sqrt((xx) + (yy) + (delta_z*delta_z));
95			// std::cerr << "abs_end " ;
96			} else {
97			distance = sqrt((xx) + (yy));
98			// std::cerr << "middle ";
99			}
100
101			bool isIT=false;
102			if ( distance <= rodRadius_ ) {
103			// cerr << "accepted!\n";
104			isIT=true;
105			} else {
106			// cerr << "rejected!\n";
107			}
108			return isIT;
109			}
110
111			}