SWNTGenerator

class sknano.generators.SWNTGenerator(*args, from_scaling_matrix=False, **kwargs)

Bases: sknano.generators.NanotubeBundleGeneratorBase, sknano.generators.SWNTGeneratorBase, sknano.core.structures.SWNT

Class for generating SWNT structures.

Parameters:

• *Ch –

  Either a 2-tuple of integers (i.e., *Ch = [(n, m)]) or 2 integers (i.e., *Ch = [n, m]) specifying the chiral indices of the nanotube chiral vector \(\mathbf{C}_h = n\mathbf{a}_1 + m\mathbf{a}_2 = (n, m)\).

• ny, nz (nx,) – Number of repeat unit cells in the \(x, y, z\) dimensions.
• basis ({list}, optional) –

  List of strs of element symbols or atomic number of the two atom basis (default: [‘C’, ‘C’])

  New in version 0.3.10.

• element2 (element1,) –

  Element symbol or atomic number of basis Atom 1 and 2

  Deprecated since version 0.3.10: Use basis instead

• bond (float, optional) – \(\mathrm{a}_{\mathrm{CC}} =\) distance between nearest neighbor atoms. Must be in units of Angstroms.
• Lz (float, optional) –

  Length of nanotube in units of Angstroms. Overrides the nz value.

  New in version 0.2.5.

  Changed in version 0.4.0: Changed units from nanometers to Angstroms

• tube_length (float, optional) –

  Length of nanotube in units of Angstroms. Overrides the nz value.

  Deprecated since version 0.2.5: Use Lz instead

• fix_Lz (bool, optional) –

  Generate the nanotube with length as close to the specified \(L_z\) as possible. If True, then non integer \(n_z\) cells are permitted.

  New in version 0.2.6.

• vdw_radius (float, optional) –

  van der Waals radius of nanotube atoms

  New in version 0.2.5.

• bundle_packing ({'hcp', 'ccp'}, optional) –

  Packing arrangement of nanotubes bundles. If bundle_packing is None, then it will be determined by the bundle_geometry parameter if bundle_geometry is not None. If both bundle_packing and bundle_geometry are None, then bundle_packing defaults to hcp.

  New in version 0.2.5.

• bundle_geometry ({'triangle', 'hexagon', 'square', 'rectangle'}, optional) –

  Force a specific geometry on the nanotube bundle boundaries.

  New in version 0.2.5.

• autogen (bool, optional) – if True, automatically generate structure data.
• verbose (bool, optional) – if True, show verbose output

Examples

Using the SWNTGenerator class, you can generate structure data for single-walled nanotubes (SWNTs) or nanotube bundles with either cubic close packed (ccp) or hexagonal close packed (hcp) arrangement of nanotubes. The bundle packing arrangement is set using the bundle_packing parameter.

You can also enforce a specific bundle geometry which will try and build the nanotube bundle such that it “fits inside” the boundaries of a specified geometric shape. This allows you to generate hcp bundles that are trianglar, hexagonal, or rectangular in shape, as some of the examples below illustrate.

First, load the SWNTGenerator class.

>>> from sknano.generators import SWNTGenerator

Now let’s generate a \(\mathbf{C}_{\mathrm{h}} = (10, 5)\) SWNT unit cell.

>>> swnt = SWNTGenerator((10, 5))
>>> swnt.save(fname='10,5_unit_cell.xyz')
>>> # note that there are two other alternative, but equivalent
>>> # means of passing arguments to SWNTGenerator constructor:
>>> # SWNTGenerator(10, 5) and SWNTGenerator(n=10, m=5)

Here’s a nice ray traced rendering of the generated \((10, 5)\) SWNT unit cell.

Next, let’s generate an hcp bundle of \(C_{\mathrm{h}} = (10, 5)\) SWCNTs and cell count \(n_x=10, n_y=3, n_z=5\).

>>> SWCNTbundle = SWNTGenerator(n=10, m=5, nx=10, ny=3, nz=5)
>>> SWCNTbundle.save()

The rendered structure looks like:

Now let’s generate a nice hexagon bundle, 3 tubes wide, with \(C_{\mathrm{h}} = (6, 5)\).

>>> SWCNTbundle = SWNTGenerator(n=6, m=5, nz=5, bundle_geometry='hexagon')
>>> SWCNTbundle.save()

which looks like:

Remember, all of the save methods allow you to rotate the structure data before saving:

>>> SWCNTbundle.save(fname='0605_hcp_7tube_hexagon_rot-30deg.xyz',
...                  rot_axis='z', rotation_angle=30)

Now, just because we can, let’s make a big ass hexagon bundle with \(C_{\mathrm{h}} = (10, 0)\).

>>> big_hexagonal_bundle = SWNTGenerator(10, 0, nx=25, ny=25, nz=1,
...                                      bundle_geometry='hexagon')
>>> big_hexagonal_bundle.save()

Take a look at the 469 \((10, 0)\) unit cells in this big ass bundle!

Lastly, here’s a look at a bundle generated with cubic close packed bundle arrangement:

>>> SWCNTbundle = SWNTGenerator(10, 10, nx=3, ny=3, nz=5,
...                             bundle_packing='ccp')
>>> SWCNTbundle.save()

The rendered ccp structure looks like:

Attributes

Ch	SWNT circumference \(|\mathbf{C}_h|\) in Å
Ch_vec	SWNT chiral vector.
Lx	Axis-aligned length along the x-axis in Angstroms.
Ly	Axis-aligned length along the y-axis in Angstroms.
Lz	SWNT length \(L_z = L_{\mathrm{tube}}\) in Angstroms.
M	\(M = np - nq\)
N	Number of graphene hexagons in nanotube unit cell.
Natoms	N atoms.
Natoms_list	list of Natoms per nanotube in bundle.
Natoms_per_bundle	Alias for Natoms.
Natoms_per_tube	Alias for Natoms_list.
Natoms_per_unit_cell	Number of atoms in nanotube unit cell.
Ntubes	Number of nanotubes in bundle.
R	Symmetry vector \(\mathbf{R} = (p, q)\).
T	Length of nanotube unit cell \(|\mathbf{T}|\) in Å.
Tvec	SWNT translation vector.
atoms	Structure Atoms.
basis	NanoStructureBase basis objects.
bundle_density	Compute the nanotube bundle density.
bundle_geometry	Bundle geometry.
bundle_mass	An alias for mass.
bundle_packing	Bundle packing.
chiral_angle	Chiral angle \(\theta_c\) in degrees.
chiral_type	SWNT chiral type.
crystal_cell	Structure CrystalCell.
d	\(d=\gcd{(n, m)}\)
dR	\(d_R=\gcd{(2n + m, 2m + n)}\)
dt	Nanotube diameter \(d_t = \frac{|\mathbf{C}_h|}{\pi}\) in Å.
electronic_type	SWNT electronic type.
element1	Basis element 1
element2	Basis element 2
fix_Lz	bool indicating whether SWNTMixin.Lz is fixed or calculated.
fmtstr	Format string.
lattice	Structure Crystal3DLattice.
lattice_shift	Lattice displacement vector.
linear_mass_density	Linear mass density of nanotube in g/Å.
m	Chiral index \(m\).
mass	Total mass of atoms.
n	Chiral index \(n\).
nx	Number of nanotubes along the \(x\)-axis.
ny	Number of nanotubes along the \(y\)-axis.
nz	Number of nanotube unit cells along the \(z\)-axis.
rt	Nanotube radius \(r_t = \frac{|\mathbf{C}_h|}{2\pi}\) in Å.
scaling_matrix	CrystalCell.scaling_matrix.
structure	An alias to self.
t1	\(t_{1} = \frac{2m + n}{d_{R}}\)
t2	\(t_2 = -\frac{2n + m}{d_R}\)
tube_length	Alias for SWNT.Lz
tube_mass	An alias for mass.
unit_cell	Structure UnitCell.
unit_cell_mass	Unit cell mass in atomic mass units.
unit_cell_symmetry_params	Tuple of SWNT unit cell symmetry parameters.
vdw_distance	Van der Waals distance.
vdw_radius	Van der Waals radius

Methods

clear()	Clear list of StructureMixin.atoms.
finalize()	Finalize structure data by clipping region bounds if fix_Lz is True.
generate([finalize])	Generate structure data.
generate_bundle_coords()	Generate coordinates of bundle tubes.
generate_fname([n, m, nx, ny, nz, fix_Lz, ...])	Generate filename string.
init_bundle_parameters()	Initialize bundle attributes.
make_supercell(scaling_matrix[, wrap_coords])	Make supercell.
rotate(**kwargs)	Rotate crystal cell lattice, basis, and unit cell.
save([fname, outpath, structure_format, ...])	Save structure data.
todict()	Return dict of constructor parameters.
transform_lattice(scaling_matrix[, ...])	Transform structure lattice.
translate(t[, fix_anchor_points])	Translate crystal cell lattice, basis, and unit cell.
write(*args, **kwargs)	Write structure data to file.
write_data(**kwargs)	Write LAMMPS data file.
write_dump(**kwargs)	Write LAMMPS dump file.
write_pdb(**kwargs)	Write pdb file.
write_xyz(**kwargs)	Write xyz file.

Methods Summary

finalize()	Finalize structure data by clipping region bounds if fix_Lz is True.
generate_fname([n, m, nx, ny, nz, fix_Lz, ...])	Generate filename string.
save([fname, outpath, structure_format, ...])	Save structure data.

Methods Documentation

finalize()

Finalize structure data by clipping region bounds if fix_Lz is True.

classmethod generate_fname(n=None, m=None, nx=None, ny=None, nz=None, fix_Lz=False, Ntubes=None, bundle_geometry=None, bundle_packing=None, **kwargs)

Generate filename string.

save(fname=None, outpath=None, structure_format=None, center_centroid=True, **kwargs)

Save structure data.

See save method for documentation.