コード例 #1
0
ファイル: _graphene.py プロジェクト: chr7stos/scikit-nano
 def __init__(self, bond=aCC, a=3 * aCC, b=np.sqrt(3) * aCC, c=2 * r_CC_vdw,
              basis=4 * ['C'],
              coords=[[0, 0, 0], [aCC, 0, 0],
                      [3 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0],
                      [5 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0]],
              cartesian=True):
     lattice = Crystal3DLattice.orthorhombic(a, b, c)
     super().__init__(lattice, basis, coords, cartesian)
コード例 #2
0
    def generate_unit_cell(self):
        """Generate the nanotube unit cell."""
        eps = 0.01

        e1 = self.element1
        e2 = self.element2
        N = self.N
        T = self.T
        rt = self.rt

        psi, tau, dpsi, dtau = self.unit_cell_symmetry_params

        a = compute_Ch(self.n, self.m, bond=self.bond)
        b = self.layer_spacing
        c = compute_T(self.n, self.m, bond=self.bond, length=True)
        lattice = Crystal3DLattice.orthorhombic(a, b, c)

        basis = Atoms()
        if self.verbose:
            print('dpsi: {}'.format(dpsi))
            print('dtau: {}\n'.format(dtau))

        for i in range(N):
            for j, element in enumerate((e1, e2), start=1):
                theta = i * psi
                h = i * tau

                if j == 2:
                    theta += dpsi
                    h -= dtau

                x = rt * theta
                z = h

                while z > T - eps:
                    z -= T

                if z < 0:
                    z += T

                xs, ys, zs = \
                    lattice.cartesian_to_fractional([x, 0, z])
                if self.wrap_coords:
                    xs, ys, zs = \
                        lattice.wrap_fractional_coordinate([xs, ys, zs])

                if self.debug:
                    print('i={}: x, z = ({:.6f}, {:.6f})'.format(i, x, z))

                atom = Atom(element, lattice=lattice, xs=xs, ys=ys, zs=zs)
                atom.rezero()

                if self.verbose:
                    print('Basis Atom:\n{}'.format(atom))

                basis.append(atom)

        self.unit_cell = UnitCell(lattice=lattice, basis=basis)
コード例 #3
0
ファイル: _graphene.py プロジェクト: haidi-ustc/scikit-nano
 def __init__(self,
              bond=aCC,
              a=3 * aCC,
              b=np.sqrt(3) * aCC,
              c=2 * r_CC_vdw,
              basis=4 * ['C'],
              coords=[[0, 0, 0], [aCC, 0, 0],
                      [3 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0],
                      [5 / 2 * aCC, np.sqrt(3) / 2 * aCC, 0]],
              cartesian=True):
     lattice = Crystal3DLattice.orthorhombic(a, b, c)
     super().__init__(lattice, basis, coords, cartesian)