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root/OpenMD/trunk/src/applications/nanoparticleBuilder/shapedLatticeRod.cpp
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Comparing trunk/src/applications/nanoparticleBuilder/shapedLatticeRod.cpp (file contents):
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC vs.
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). *
40 > * [4]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41 > */
42 >
43 > /*
44   *  Created by Kelsey M. Stocker on 2/9/12.
45   *  @author  Kelsey M. Stocker
46   *  @version $Id: shapedLatticeRod.cpp 1665 2011-11-22 20:38:56Z gezelter $
# Line 53 | Line 56 | namespace OpenMD {
56    
57    shapedLatticeRod::shapedLatticeRod(RealType latticeConstant,
58                                       std::string latticeType,
59 <                                     RealType radius, RealType length) : shapedLattice(latticeConstant, latticeType){
59 >                                     RealType radius,
60 >                                     RealType length) : shapedLattice(latticeConstant, latticeType){
61      
62      rodRadius_= radius;
63      rodLength_= length;
60 –
64      Vector3d dimension;
65      dimension[0] = 3.0*radius;
66      dimension[1] = 3.0*radius;
67      dimension[2] = length + 3.0*radius;
65 –    cerr << "using dimension = " << dimension << "\n";
68      setGridDimension(dimension);
67 –    cerr << "done!\n";
69      Vector3d origin;
70      origin[0] = 0;
71      origin[1] = 0;
# Line 72 | Line 73 | namespace OpenMD {
73      setOrigin(origin);
74    }
75  
75 –
76    /**
77 <   * Determines whether a point lies within a spherically-capped nanorod at origin (0,0,0)
77 >   * Determines whether a point lies within a spherically-capped
78 >   * nanorod at origin (0,0,0)
79     *
80     */
80 –
81    bool shapedLatticeRod::isInterior(Vector3d point){
82  
83 <    RealType x, y, z, distance, delta_z;
83 >    RealType x, y, z, distance;
84  
85      distance = 0;
86      
87      x = point[0];
88      y = point[1];
89      z = point[2];
90 –    //  std::cerr << "Testing xyz = " << point << " \n";
90      
91      if ( abs(z) >= rodLength_/2.0 ) {
92 <      delta_z = abs(z) - rodLength_/2.0;
92 >      RealType delta_z = abs(z) - rodLength_/2.0;
93        distance = sqrt((x*x) + (y*y) + (delta_z*delta_z));
95 –      //    std::cerr << "abs_end " ;
94      } else {
95        distance = sqrt((x*x) + (y*y));
98 –      //   std::cerr << "middle ";
96      }
97      
98      bool isIT=false;
99      if ( distance <= rodRadius_ ) {
103 –      //   cerr << "accepted!\n";
100        isIT=true;
105 –    } else {
106 –      //     cerr << "rejected!\n";
101      }
102      return isIT;
103    }

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