esta.spaceGroup package#

Submodules#

esta.spaceGroup.read_cif module#

esta.spaceGroup.read_cif.cif(inputfile)#: read cif and generate all atoms through sym op. privided in the cif file as well as other atom and cell parameters to describe the xtal structure

esta.spaceGroup.transform module#

class esta.spaceGroup.transform.Transform(cryst_obj)#

Bases: object

transfor class to: -create supercell from crystal lattice object -rotation/translation etc… -
More transformations to: -unit cell/atomic positions/reciprocal lattice/kpoints to be added

author: sk email: sonukumar.physics@gmail.com

get_grouped_xyz()#: xyz file with grouped atoms of same type

get_neach_type(inp)#: get number of list entries of each type

list of strings of atomic labels

get integer number of list entries (atomic symbols) of each type

get_sposcar()#: get poscar file with scaled dimensions: supercell of POSCAR file

get_supercell(scale)#

create supercell by shifting ALL atoms in space with scaling

[scale1,scale2,scale3]

looping is performed along three directions of lv’s vectors
loops are:
i = 0,1,2 … sclae1 j = 0,1,2 … scale2 k = 0,1,2 … scale3
total atoms in supercell = atoms in unit-cell * np.product([scale1,scale2,scale3])

rot_trans(inp_mat, lcell=None, lposition=None, translation=None, rotation_matrix=None)#

given input matrix (may be cell matrix or position matrix in c order) and rotation matrix (optional; default is unit matrix), output respective new matrix

Parameters

inp_mat (array; rank 3 or rank N (no. of atoms)) –
lcell (logical, indicates inp_mat is for cell) –
lposition (logical, indicates that inp_mat is for atomic points/positions) –
1 (translation; array/vecor; rank) –
0)) (optional (default is zero vector = (0 0) –
rotation_matrix (array of rank3, optional (default is unit matrix)) –

Return type

inp_mat like

Note: following convention like spglib: https://spglib.github.io/spglib/definition.html

====> Basis vectors (a,b,c) or (a1, a2, a3)

In spglib, basis vectors are represented by three column vectors (in Cartesian coordinates. ) :

a=⎛⎝⎜ax ay az⎞⎠⎟, b=⎛⎝⎜bx by bz⎞⎠⎟, c=⎛⎝⎜cx cy cz⎞⎠⎟,

====> atomic point x are represented as three fractional values relative to basis vectors as follows,

x=⎛⎝⎜x1x2x3⎞⎠⎟

====> The transformation matrix P changes choice of basis vectors as follows

(a b c) = (as bs cs) P where (abc) and (as bs cs) are the basis vectors of an arbitrary system and of a starndardized system, respectively

The origin shift p gives the vector from the origin of the standardized system Os to the origin of the arbitrary system O p = O − Os

A change of basis is described by the combination of the transformation matrix and the origin shift denoted by (P,p) where first the transformation matrix is applied and then origin shift. The points in the standardized system xs and arbitrary system x are related by

xs = P x + p,

or equivalently,

x = P^-1 xs − P^-1 p

esta.spaceGroup.transform_adv module#

class esta.spaceGroup.transform_adv.transform(cryst_obj)#