Decahedron.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 "clusters/Decahedron.hpp"
 
#include <algorithm>
#include <cmath>
 
#include "utils/Constants.hpp"
 
using namespace std;
 
namespace OpenMD {
 
  Decahedron::Decahedron(int columnAtoms, int shells, int twinAtoms) :
      N_(columnAtoms), M_(shells), K_(twinAtoms) {
    Basis.clear();
    Points.clear();
 
    //
    // Initialize Basis vectors.
    //
    const RealType phi  = 2.0 * Constants::PI / 5.0;  // 72 degrees
    const RealType r3o2 = 0.5 * sqrt(3.0);
 
    Basis.push_back(
        Vector3d(r3o2 * cos(0.0 * phi), r3o2 * sin(0.0 * phi), 0.0));
    Basis.push_back(
        Vector3d(r3o2 * cos(1.0 * phi), r3o2 * sin(1.0 * phi), 0.0));
    Basis.push_back(
        Vector3d(r3o2 * cos(2.0 * phi), r3o2 * sin(2.0 * phi), 0.0));
    Basis.push_back(
        Vector3d(r3o2 * cos(3.0 * phi), r3o2 * sin(3.0 * phi), 0.0));
    Basis.push_back(
        Vector3d(r3o2 * cos(4.0 * phi), r3o2 * sin(4.0 * phi), 0.0));
  }
 
  vector<Vector3d> Decahedron::getPoints() {
    // Generate central column of Decahedron
 
    for (int i = 0; i < N_; i++) {
      Points.push_back(Vector3d(0.0, 0.0, RealType(i) - 0.5 * (N_ - 1)));
    }
 
    for (int i = 1; i < M_ + 1; i++) {
      // generate the shells of the decahedron:
 
      vector<Vector3d> ring;
 
      if (i > K_ - 1) {
        ring = truncatedRing(i, i - K_ + 1);
      } else {
        ring = truncatedRing(i, 0);
      }
 
      // shift the rings in the z-direction (along the shell)
 
      for (int j = 0; j < N_ - i; j++) {
        Vector3d shift =
            Vector3d(0, 0, -0.5 * RealType((N_ - i) - 1) + RealType(j));
 
        for (vector<Vector3d>::iterator k = ring.begin(); k != ring.end();
             ++k) {
          Points.push_back((*k) + shift);
        }
      }
    }
    return Points;
  }
 
  vector<Vector3d> Decahedron::truncatedRing(int n, int k) {
    // This function generates the rings of a Decahedron
    // n: index of shell (order of ring)
    // k: how many atoms are missing from both ends of one side of
    //    pentagon ring
 
    vector<Vector3d> ring;
 
    // Generate atomic coordinates along each side of pentagonal ring
    for (int i = 0; i < 5; i++) {
      Vector3d b1 = Basis[i];
      Vector3d b2 = Basis[(i + 1) % 5];
 
      if (k == 0) {
        // without truncation
        for (int j = 0; j < n; j++) {
          ring.push_back(RealType(n) * b1 + RealType(j) * (b2 - b1));
        }
 
      } else {
        for (int j = k; j <= n - k; j++) {
          // with truncation
          ring.push_back(RealType(n) * b1 + RealType(j) * (b2 - b1));
        }
      }
    }
    return ring;
  }
 
  CurlingStoneDecahedron::CurlingStoneDecahedron(int columnAtoms, int shells,
                                                 int twinAtoms,
                                                 int truncatedPlanes) :
      Decahedron(columnAtoms, shells, twinAtoms),
      T_(truncatedPlanes) {}
 
  vector<Vector3d> CurlingStoneDecahedron::getPoints() {
    vector<Vector3d> raw = Decahedron::getPoints();
    vector<Vector3d> snipped;
    RealType maxZ, minZ;
 
    maxZ = raw.begin()->z();
    minZ = raw.begin()->z();
 
    for (vector<Vector3d>::iterator i = raw.begin(); i != raw.end(); ++i) {
      maxZ = max(maxZ, (*i).z());
      minZ = min(minZ, (*i).z());
    }
 
    for (vector<Vector3d>::iterator i = raw.begin(); i != raw.end(); ++i) {
      if (((*i).z() < maxZ - 0.995 * (T_ / 2.0)) &&
          ((*i).z() > minZ + 0.995 * (T_ / 2.0))) {
        snipped.push_back((*i));
      }
    }
    return snipped;
  }
 
}  // namespace OpenMD