viperleed.calc.classes.slab.bulk_slab.BulkSlab

class viperleed.calc.classes.slab.bulk_slab.BulkSlab

A class representing an infinite solid, period in 3D.

Contains unit cell, element information and atom coordinates. Also has a variety of convenience functions for manipulating and updating the atoms.

ucell

The unit cell as vectors a, b, c (columns)

Type:

np.array

poscar_scaling

The original scaling factor from POSCAR

Type:

float

elements

Element labels as read from POSCAR

Type:

tuple of str

chemelem

Chemical elements in the slab, including from ELEMENT_MIX

Type:

set of str

n_per_elem

The number of atoms per POSCAR element.

Type:

dict {str: int}

atlist

List of all atoms in the slab.

Type:

AtomList

layers

Each layer is a composite of sublayers, as in TensErLEED

Type:

tuple of Layer

sublayers

Each SubLayer contains atoms of equal element and Z coordinate

Type:

tuple of SubLayer

sitelist

List of distinct sites as Sitetype, storing information on vibration and concentration

Type:

list of Sitetype

ucell_mod

Stored modifications made to the unit cell; each is a tuple of (type, array), where type is ‘lmul’, ‘rmul’, ‘add’, or ‘c_shift’.

Type:

list of tuples (str, numpy.ndarray)

topat_ori_z

Stores the original position of the topmost atom in Cartesian coordinates

Type:

float

celltype

Unit-cell shape as string. Values: ‘oblique’, ‘rhombic’, ‘rectangular’, ‘square’, ‘hexagonal’

Type:

str # TODO: would be nicer with an Enum

planegroup

Symmetry group of the slab. May be reduced by the user relative to foundplanegroup.

Type:

str

foundplanegroup

Highest symmetry found. Doesn’t get modified when user reduces symmetry manually.

Type:

str

orisymplane

Only stored if the planegroup is ambiguous as to which unit vector the symmetry plane at the origin is parallel to

Type:

SymPlane

linklists

List of lists of atoms which are linked by a symmetry operation

Type:

list of list of Atom

bulk_screws

Integer list of rotation orders present in the bulk.

Type:

list of int

bulk_glides

List of glide-symmetry planes present in the bulk.

Type:

list of SymPlane

__init__()

Initialize instance.

Methods

__init__()	Initialize instance.
apply_bulk_cell_reduction(eps[, epsz, ...])	Reduce bulk unit cell in- and/or out-of-plane.
apply_matrix_transformation(trafo_matrix)	Apply an orthogonal transformation to the unit cell and all atoms.
apply_scaling(*scaling)	Rescale the unit-cell vectors.
check_a_b_in_plane()	Raise InvalidUnitCellError if a, b have out-of-plane components.
clear_symmetry_and_ucell_history()	Set all symmetry information back to default values.
collapse_cartesian_coordinates([update_origin])	Ensure all atoms are inside the unit cell.
collapse_fractional_coordinates([releps])	Ensure all atoms are inside the unit cell.
create_layers(rpars[, bulk_cuts])	Create a list of Layer objects based on rpars.
create_sublayers([eps])	Assign the atoms in the slab to sublayers.
ensure_minimal_c_vector(rpars[, z_periodic])	Reduce the c vector to its minimum value.
from_slab(other)	Return a cls instance with attributes deep-copied from other.
full_update(rpars)	Update atoms and layers from rpars.
get_bulk_3d_str()	Return info about bulk screw axes and glide planes as a string.
get_bulk_repeat(rpars[, only_z_distance])	Return the bulk repeat vector (with positive z).
get_candidate_layer_periods([epsz])	Find at which offsets the sublayers repeat in a bulk slab.
get_minimal_ab_cell(eps[, epsz, warn_convention])	Check if there is a 2D unit cell smaller than the current one.
get_minimal_c_vector(eps[, epsz, z_periodic])	Return the smallest bulk c vector, if any.
initSites(rp)	Goes through the atom list and supplies them with appropriate SiteType objects, based on the SITE_DEF parameters from the supplied Rparams.
is_bulk_glide_symmetric(symplane, ...)	Return if the slab has a 3D glide plane.
is_bulk_screw_symmetric(order, ...)	Return if the slab has a 3D screw axis.
is_equivalent(other[, eps])	Return whether this slab is equivalent to another.
is_mirror_symmetric(symplane, eps[, glide])	Return if this slab is unchanged when applying a 2D mirror/glide.
is_rotation_symmetric(axis, order, eps)	Return if this slab is unchanged when applying a 2D rotation.
is_translation_symmetric(translation, eps[, ...])	Return if this slab is unchanged when translated.
mirror_atoms(symplane[, glide])	Apply a mirror or glide transform across symplane.
project_c_to_z()	Make the c vector of the unit cell perpendicular to the surface.
remove_duplicate_atoms([eps, epsz, other_slab])	Remove atoms with same positions and chemical element.
remove_vacuum_at_bottom(rpars)	Move all atoms along c to remove any vacuum at the bottom.
revert_unit_cell([restore_to])	Revert unit-cell and coordinate modifications.
rotate_atoms(order[, axis])	Apply an order-fold 2D rotation around axis.
rotate_unit_cell(order[, append_ucell_mod])	Rotate the unit cell around the origin.
sort_by_element()	Sort slab.atlist by element, preserving the element order.
sort_by_z([bottom_to_top])	Sort slab.atlist by z coordinate.
sort_original()	Sort slab.atlist by original atom order from POSCAR.
transform_unit_cell_2d(transform[, ...])	Apply a 2D-transformation matrix to the unit cell.
translate_atoms_2d(shift)	Add a 2D Cartesian shift to all atomic coordinates.
translate_atoms_c(c_fraction)	Move all atoms up by c_fraction along the c vector.
update_atom_numbers()	Assign new incremental numbers to atoms in the slab.
update_cartesian_from_fractional([update_origin])	Assign absolute Cartesian coordinates to all atoms.
update_element_count()	Update the number of atoms per element.
update_fractional_from_cartesian()	Calculate atoms' fractional coordinates from Cartesian ones.
update_layer_coordinates()	Update the Cartesian position of all layers.
with_double_thickness([new_atoms_start_idx])	Return a copy of this bulk slab which is twice as thick.

Attributes

ab_cell	Return the 2D portion of the unit cell.
angle_between_ucell_and_coord_sys	Return angle between first unit-cell vector and coordinate system.
bottom_atom	Return the atom currently at the bottom of this slab.
bulk_atoms	Return atoms in this Slab that belong to its bulk.
bulk_layers	Return the layers of self that are bulk.
c_vector	Return the out-of-plane unit-cell vector.
elements	Return a tuple of elements in this slab, as originally read.
fewest_atoms_sublayer	Return the sublayer with fewest atoms.
interlayer_gaps	Return the z distances between pairs of adjacent layers.
is_bulk	Return whether this is a bulk slab.
n_atoms	Return the number of atoms in this slab.
n_layers	Return the number of composite layers of this slab.
n_sublayers	Return the number of sublayers in this slab.
non_bulk_layers	Return a tuple of the non-bulk layers in this slab.
smallest_interlayer_gap	Return the smallest z gap between two adjacent layers.
top_atom	Return the atom currently at the bottom of this slab.