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;

    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:	1793
Committed:	Fri Aug 31 21:16:10 2012 UTC (12 years, 8 months ago) by gezelter
File size:	3864 byte(s)
Log Message:	Cleaning up some warning messages on linux
#	Content
1	/*
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
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	}