shapedLatticePentRod.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "shapedLatticePentRod.hpp"
 
#include <cmath>
 
#include "lattice/shapedLattice.hpp"
#include "shapedLatticeRod.hpp"
 
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;
    setGridDimension(dimension);
    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;
  }
}  // namespace OpenMD