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root/OpenMD/trunk/src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp
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Comparing:
branches/development/src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp (file contents), Revision 1701 by kstocke1, Thu Apr 5 19:37:58 2012 UTC vs.
trunk/src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp (file contents), Revision 1977 by gezelter, Wed Mar 12 21:35:23 2014 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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.
# Line 58 | Line 58 | namespace OpenMD {
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;                                  
61      Vector3d dimension;
62      dimension[0] = 2.0*length;
63      dimension[1] = 2.0*length;
64      dimension[2] = 2.0*length;
67 –    cerr << "using dimension = " << dimension << "\n";
65      setGridDimension(dimension);
69 –    cerr << "done!\n";
66      Vector3d origin;
67      origin[0] = 0;
68      origin[1] = 0;
# Line 83 | Line 79 | namespace OpenMD {
79    bool shapedLatticePentRod::isInterior(Vector3d point){
80  
81      RealType x, y, z, new_x, new_y, left_newx, right_newx;
82 <    int z_int;
82 >    // int z_int;
83  
84      bool isIT=false;
85  
# Line 91 | Line 87 | namespace OpenMD {
87      y = point[1];
88      z = point[2];
89  
90 <    z_int = z/2.04;
90 >    // z_int = int(z/2.04);
91  
92      //Rotate by 45 degrees around z-axis so length of rod lies along y axis
93 <    new_x = (sqrt(2)/2)*(x - y);
94 <    new_y = (sqrt(2)/2)*(x + y);
93 >    new_x = (sqrt(2.0)/2)*(x - y);
94 >    new_y = (sqrt(2.0)/2)*(x + y);
95  
96      left_newx = (z - 1.44)*(0.577350269/0.816496581);
97      right_newx = (z + 1.44)*(-0.577350269/0.816496581);

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