applications/nanoparticleBuilder/shapedLatticePentRod.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 "shapedLatticePentRod.hpp"
#include "shapedLatticeRod.hpp"
#include <cmath>

using namespace std;
namespace OpenMD {
  
  shapedLatticePentRod::shapedLatticePentRod(RealType latticeConstant,
                                     std::string latticeType, 
                                     RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){
    
    rodRadius_= radius;
    rodLength_= length;
    double x, y, z, new_x, new_y, new_z, new_x72, new_z72, left_newx, right_newx, left_newx72, right_newx72;
    int z_int;                                  
    Vector3d dimension;
    dimension[0] = 2.0*length;
    dimension[1] = 2.0*length;
    dimension[2] = 2.0*length;
    cerr << "using dimension = " << dimension << "\n";
    setGridDimension(dimension);
    cerr << "done!\n";
    Vector3d origin;
    origin[0] = 0;
    origin[1] = 0;
    origin[2] = 2.04;
    setOrigin(origin);
  }


  /**
   * Creates a wedge for pentagonal nanorods
   *
   */ 

  bool shapedLatticePentRod::isInterior(Vector3d point){

    RealType x, y, z, new_x, new_y, left_newx, right_newx;
    int z_int;

    bool isIT=false;

    x = point[0];
    y = point[1];
    z = point[2];

    z_int = z/2.04;

    //Rotate by 45 degrees around z-axis so length of rod lies along y axis
    new_x = (sqrt(2.0)/2)*(x - y);
    new_y = (sqrt(2.0)/2)*(x + y);
 
    left_newx = (z - 1.44)*(0.577350269/0.816496581);
    right_newx = (z + 1.44)*(-0.577350269/0.816496581);

    //Make center spine of nanorod down new_y axis
    //This is now done directly in nanorod_pentBuilder.cpp
    /*if ( (new_x == 0) && (z == 0) ) {

      if ( abs(new_y) <= 0.5*rodLength_ + 0.5773502692*rodRadius_ ) {

        isIT = true;

      }  
      }*/

    //Make one wedge
    if ( (z < 0) && (z >= -0.816496581*rodRadius_ - 1.44) ) {
      
      if ( abs(new_y) <= 1.44*(z/2.04) + 0.5*rodLength_ + 0.5773502692*rodRadius_ ) { 
        
        if ( (new_x >= left_newx) && (new_x <= right_newx) ) {
          
          isIT=true;
          
        }         
      }
    }      
    return isIT;
  }
}
Revision:	1767
Committed:	Fri Jul 6 22:01:58 2012 UTC (12 years, 9 months ago) by gezelter
File size:	4337 byte(s)
Log Message:	Various fixes required to compile OpenMD with the MS Visual C++ compiler
#	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 "shapedLatticePentRod.hpp"
49	#include "shapedLatticeRod.hpp"
50	#include <cmath>
51
52	using namespace std;
53	namespace OpenMD {
54
55	shapedLatticePentRod::shapedLatticePentRod(RealType latticeConstant,
56	std::string latticeType,
57	RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){
58
59	rodRadius_= radius;
60	rodLength_= length;
61	double x, y, z, new_x, new_y, new_z, new_x72, new_z72, left_newx, right_newx, left_newx72, right_newx72;
62	int z_int;
63	Vector3d dimension;
64	dimension[0] = 2.0*length;
65	dimension[1] = 2.0*length;
66	dimension[2] = 2.0*length;
67	cerr << "using dimension = " << dimension << "\n";
68	setGridDimension(dimension);
69	cerr << "done!\n";
70	Vector3d origin;
71	origin[0] = 0;
72	origin[1] = 0;
73	origin[2] = 2.04;
74	setOrigin(origin);
75	}
76
77
78	/**
79	* Creates a wedge for pentagonal nanorods
80	*
81	*/
82
83	bool shapedLatticePentRod::isInterior(Vector3d point){
84
85	RealType x, y, z, new_x, new_y, left_newx, right_newx;
86	int z_int;
87
88	bool isIT=false;
89
90	x = point[0];
91	y = point[1];
92	z = point[2];
93
94	z_int = z/2.04;
95
96	//Rotate by 45 degrees around z-axis so length of rod lies along y axis
97	new_x = (sqrt(2.0)/2)*(x - y);
98	new_y = (sqrt(2.0)/2)*(x + y);
99
100	left_newx = (z - 1.44)*(0.577350269/0.816496581);
101	right_newx = (z + 1.44)*(-0.577350269/0.816496581);
102
103	//Make center spine of nanorod down new_y axis
104	//This is now done directly in nanorod_pentBuilder.cpp
105	/*if ( (new_x == 0) && (z == 0) ) {
106
107	if ( abs(new_y) <= 0.5rodLength_ + 0.5773502692rodRadius_ ) {
108
109	isIT = true;
110
111	}
112	}*/
113
114	//Make one wedge
115	if ( (z < 0) && (z >= -0.816496581*rodRadius_ - 1.44) ) {
116
117	if ( abs(new_y) <= 1.44(z/2.04) + 0.5rodLength_ + 0.5773502692*rodRadius_ ) {
118
119	if ( (new_x >= left_newx) && (new_x <= right_newx) ) {
120
121	isIT=true;
122
123	}
124	}
125	}
126	return isIT;
127	}
128	}