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;
    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 = 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:	1796
Committed:	Mon Sep 10 18:38:44 2012 UTC (12 years, 7 months ago) by gezelter
File size:	4219 byte(s)
Log Message:	Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft
#	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 "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			Vector3d dimension;
62			dimension[0] = 2.0*length;
63			dimension[1] = 2.0*length;
64			dimension[2] = 2.0*length;
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] = 2.04;
72			setOrigin(origin);
73			}
74
75
76			/**
77			* Creates a wedge for pentagonal nanorods
78			*
79			*/
80
81			bool shapedLatticePentRod::isInterior(Vector3d point){
82
83			RealType x, y, z, new_x, new_y, left_newx, right_newx;
84	gezelter	1796	// int z_int;
85	kstocke1	1701
86			bool isIT=false;
87
88			x = point[0];
89			y = point[1];
90			z = point[2];
91
92	gezelter	1796	// z_int = int(z/2.04);
93	kstocke1	1701
94			//Rotate by 45 degrees around z-axis so length of rod lies along y axis
95	gezelter	1767	new_x = (sqrt(2.0)/2)*(x - y);
96			new_y = (sqrt(2.0)/2)*(x + y);
97	kstocke1	1701
98			left_newx = (z - 1.44)*(0.577350269/0.816496581);
99			right_newx = (z + 1.44)*(-0.577350269/0.816496581);
100
101			//Make center spine of nanorod down new_y axis
102			//This is now done directly in nanorod_pentBuilder.cpp
103			/*if ( (new_x == 0) && (z == 0) ) {
104
105			if ( abs(new_y) <= 0.5rodLength_ + 0.5773502692rodRadius_ ) {
106
107			isIT = true;
108
109			}
110			}*/
111
112			//Make one wedge
113			if ( (z < 0) && (z >= -0.816496581*rodRadius_ - 1.44) ) {
114
115			if ( abs(new_y) <= 1.44(z/2.04) + 0.5rodLength_ + 0.5773502692*rodRadius_ ) {
116
117			if ( (new_x >= left_newx) && (new_x <= right_newx) ) {
118
119			isIT=true;
120
121			}
122			}
123			}
124			return isIT;
125			}
126			}