Single crystalline particle¶
- class wulffpack.SingleCrystal(surface_energies, primitive_structure=None, natoms=1000, tol=1e-05)[source]¶
A SingleCrystal object is a Wulff construction of a single crystalline particle, i.e., a standard Wulff construction.
- Parameters
surface_energies (
dict
) – A dictionary with surface energies, where keys are Miller indices and values surface energies (per area) in a unit of choice, such as J/m^2.primitive_structure (
Optional
[Atoms
]) – primitive cell to implicitly define the point group as well as the atomic structure used if an atomic structure is requested. By default, an Au FCC structure is used.natoms (
int
) – Together with primitive_structure, this parameter defines the volume of the particle. If an atomic structure is requested, the number of atoms will as closely as possible match this value.tol (
float
) – Numerical tolerance parameter.
Example
The following example illustrates some possible uses of a SingleCrystal object:
>>> from wulffpack import SingleCrystal >>> from ase.build import bulk >>> from ase.io import write >>> surface_energies = {(1, 1, 0): 1.0, (1, 0, 0): 1.08} >>> prim = bulk('W', a=3.16, crystalstructure='bcc') >>> particle = SingleCrystal(surface_energies, prim) >>> particle.view() >>> write('single_crystal.xyz', particle.atoms) # Writes atomic structure to file
- property area: float¶
Returns total area of the surface of the particle (not including twin boundaries).
- Return type
- property atoms: ase.atoms.Atoms¶
Returns an ASE Atoms object
- Return type
Atoms
- property average_surface_energy: float¶
Average surface energy for the Wulff construction, i.e., a weighted average over all the facets, where the weights are the area fraction of each facet.
- Return type
- property facet_fractions: Dict[tuple, float]¶
Returns a dict specifying fraction of each form (not including twin boundaries).
- property forms: List[wulffpack.core.form.Form]¶
List of inequivalent forms for the particle
- get_continuous_color_scheme(base_colors=None, normalize=False)¶
Returns a dictionary with RGB colors for each form. The colors smoothly interpolate between three base colors, corresponding to (1, 1, 1), (1, 1, 0) and (1, 0, 0). Note that this is sensible primarily for cubic systems.
- Parameters
- Return type
- get_shifted_atoms(center_shift=None)[source]¶
Returns an ASE Atoms object where the center has been shifted from with respect to the standardized cells. This can, for example, allow creation of atomistic representations in which the center of the nanoparticle does not coincide with an atom. Thereby the space of possible atomistic representations increases and may make the returned number of atoms closer to the requested number.
- make_plot(ax, alpha=0.85, linewidth=0.3, colors=None)¶
Plot a particle in an axis object. This function can be used to make customized plots of particles.
- Parameters
Example
In the following example, three different particles are plotted in the same figure:
>>> from wulffpack import SingleCrystal, Decahedron, Icosahedron >>> import matplotlib.pyplot as plt >>> from mpl_toolkits.mplot3d import Axes3D >>> >>> surface_energies = {(1, 1, 1): 1.0, ... (1, 0, 0): 1.1, ... (1, 1, 0): 1.15, ... (3, 2, 1): 1.15} >>> twin_energy = 0.05 >>> >>> fig = plt.figure(figsize=(3*4.0, 4.0)) >>> ax = fig.add_subplot(131, projection='3d') >>> particle = SingleCrystal(surface_energies) >>> particle.make_plot(ax) >>> >>> ax = fig.add_subplot(132, projection='3d') >>> particle = Decahedron(surface_energies, ... twin_energy=0.05) >>> particle.make_plot(ax) >>> >>> ax = fig.add_subplot(133, projection='3d') >>> particle = Icosahedron(surface_energies, ... twin_energy=0.05) >>> particle.make_plot(ax) >>> >>> plt.subplots_adjust(top=1, bottom=0, left=0, ... right=1, wspace=0, hspace=0) >>> plt.savefig('particles.png')
- property natoms: List[int]¶
The approximate number of atoms in the particle (implicitly defining the volume).
- property number_of_corners: float¶
Returns the number of corners (vertices) on the particle.
- Return type
- rotate_particle(rotation)¶
Rotate the particle.
- Parameters
rotation (
ndarray
) – Rotation matrix
- property standardized_structure: ase.atoms.Atoms¶
The standardized atomic structure that defines the geometry and thus the meaning of the Miller indices. Also forms the building blocks when particle.atoms is called.
- Return type
Atoms
- property surface_energy: float¶
The total surface energy of the particle (including twin boundaries).
- Return type
- translate_particle(translation)¶
Translate the particle.
- Parameters
translation (list of 3 floats) – Translation vector
- view(alpha=0.85, linewidth=0.3, colors=None, legend=True, save_as=None)¶
Use matplotlib to view a rendition of the particle.
- Parameters
alpha (
float
) – Opacity of the faceslinewidth (
float
) – Thickness of lines between facescolors (
Optional
[dict
]) – Allows custom colors for facets of all or a subset of forms, example {(1, 1, 1): ‘#FF0000’}legend (
bool
) – Whether or not to show a legend with facet-color definitionssave_as (
Optional
[str
]) – Filename to save figure as. If None, show the particle with the GUI instead.