shapedLatticeRod.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).
 */
 
/*
 *  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 "shapedLatticeRod.hpp"
 
#include <cmath>
 
#include "lattice/shapedLattice.hpp"
 
using namespace std;
namespace OpenMD {
 
  shapedLatticeRod::shapedLatticeRod(RealType latticeConstant,
                                     std::string latticeType, RealType radius,
                                     RealType length) :
      shapedLattice(latticeConstant, latticeType) {
    rodRadius_ = radius;
    rodLength_ = length;
    Vector3d dimension;
    dimension[0] = 3.0 * radius;
    dimension[1] = 3.0 * radius;
    dimension[2] = length + 3.0 * radius;
    setGridDimension(dimension);
    Vector3d origin;
    origin[0] = 0;
    origin[1] = 0;
    origin[2] = 0;
    setOrigin(origin);
  }
 
  /**
   * Determines whether a point lies within a spherically-capped
   * nanorod at origin (0,0,0)
   *
   */
  bool shapedLatticeRod::isInterior(Vector3d point) {
    RealType x, y, z, distance;
 
    distance = 0;
 
    x = point[0];
    y = point[1];
    z = point[2];
 
    if (abs(z) >= rodLength_ / 2.0) {
      RealType delta_z = abs(z) - rodLength_ / 2.0;
      distance         = sqrt((x * x) + (y * y) + (delta_z * delta_z));
    } else {
      distance = sqrt((x * x) + (y * y));
    }
 
    bool isIT = false;
    if (distance <= rodRadius_) { isIT = true; }
    return isIT;
  }
 
}  // namespace OpenMD