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operation

esta.general.operation

Transform

transfor class to * create supercell from crystal lattice object * rotation/translation etc...todo * .. * ..

  • More transformations to unit cell/atomic positions/reciprocal lattice/kpoints to be added

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

__init__(cryst_obj)

cryst_obj is
crystal_lattice.CrystalLattice('POSCAR', './') object from inout of vasp_bag

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])

get_unique_list(inp)

get unique elements of list

input: string: atomic labels
returns: string: uqique atomic labels for each type of atoms

get_grouped_list(llist)

get same string elements of list grouped together

get_neach_type(inp)

get number of list entries of each type

input: 
 list of strings of atomic labels
returns: 
get integer number of list entries (atomic symbols) of each type

get_grouped_xyz()

xyz file with grouped atoms of same type

get_sposcar()

get poscar file with scaled dimensions: supercell of POSCAR file

input: instantiate the transform class, rest is done itself
output: SPOSCAR file

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, N is no. of atoms.

  • lcell (logical, default: None ) –

    indicates inp_mat is for cell

  • lposition (logical, default: None ) –

    indicates that inp_mat is for atomic points/positions

  • translation (array, default: None ) –

    rank 1, optional (default is zero vector = (0 0 0))

  • rotation_matrix (array of rank3, default: None ) –

    rotation matrix; default is unit matrix

Returns:

  • out_mat ( array ) –

    output matrix of same shape as that of input matrix

  • .. note:: –

    following convention like spglib: .. _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