crystal_lattice_stable19072026

`esta.vaspBag.inout.crystal_lattice_stable19072026` ¶

`CrystalLattice` ¶

Crystal lattice class to define lattice parameters and basis; crystal = lattice + basis (atoms or molecules )

Author: Sonu Kumar Email: sonukumar.physics@gmail.com

`to_cartesian` `property` ¶

get atomic position in cartesin cooridnates

`to_crystal` `property` ¶

get atomic position in crystal cooridnates

`is_crystal` `property` ¶

check if atom positions in crytal coordinates

`is_cartesian` `property` ¶

check if atom positions in cartesian coordinates

`get_rVolume` `property` ¶

get real space lattice volume

`get_volume` `property` ¶

get real space lattice volume

`get_cell_vectors` `property` ¶

geta tuple of set of three cell/lattice vectors lv1, lv2, and lv3 in c-style format

`get_cell_matrix` `property` ¶

get lattice matrix of three cell/lattice vectors lv1, lv2, and lv3 in c-style format or fortran stype format default is c style format.

`cell_matrixx` `property` ¶

get lattice matrix of three cell/lattice vectors lv1, lv2, and lv3 in c-style format or fortran stype format default is c style format.

`get_atm_type` `property` ¶

get symbolic representation of atoms of each type in the form of list

`get_natm_type` `property` ¶

get no. of atoms of each type in a list format

`get_each_atm_type` `property` ¶

get same integer for atoms of same type

`is_selective_dynamics` `property` ¶

check whether selective dynamics True or False

`get_cell_angle` `property` ¶

Calculates the alpha, beta, and gamma angles (in degrees) of a cell matrix. Assumes rows are the lattice vectors a, b, and c.

`get_atm_symbol` `property` ¶

by reading POSCAR, find the atomic labels of the atoms

`read_poscar_adv(verbosity=None)` ¶

read poscar file present in the current dir or in the location specified.

parameters crysatal lattice object

return if l_SelectDynamics: return self.tau_cartesian, self.real_volume, self.LV1, self.LV2, self.LV3,self.atm_type, self.natm_type, self.natm, self.atomFix, self.atomMove, self.atomFixDir else: return self.tau_cartesian, self.real_volume, self.LV1, self.LV2, self.LV3,self.atm_type, self.natm_type, self.natm

`read_poscar(verbosity=None)` ¶

read poscar file present in the current dir or in the location specified.

parameters crysatal lattice object

return if l_SelectDynamics: return self.tau_cartesian, self.real_volume, self.LV1, self.LV2, self.LV3,self.atm_type, self.natm_type, self.natoms, self.atomFix, self.atomMove else: return self.tau_cartesian, self.real_volume, self.LV1, self.LV2, self.LV3,self.atm_type, self.natm_type, self.natoms

`set_atm_position(new_positions)` ¶

Safely updates the atomic positions array.

`set_cell_matrix(new_matrix)` ¶

Safely updates the 3x3 lattice/cell matrix.

`set_atm_symbol(new_symbol)` ¶

Safely updates the list of atomic chemical symbols.

`set_atm_fix_dir(indices, direction=None)` ¶

Parametes

indices: integers with numbering from 0 ==> atm_fix, atom_move have numbering from 0 direction: list of boolen. set atom indices as fixed (T T T vs F F F in the POSCAR file). direction is list of boolen each of len3, e.g. [[False, False, True], [..]]

Returns:

resetted values of self.atm_fix, self.atm_move, and self.atm_fix_dir for selective dynamics –

`apply_basis_rotation_(M)` ¶

Apply any 3x3 transformation matrix to the cell and atomic positions. Apply any 3x3 transformation matrix to the cell and atomic positions.

Generally the M is given row wise* in python world

_note:: M's transpose in general for passive transformation of pand p column vectors: p = M.t * p
M transpose bcz M = [[vector a ..], [vector b ..], [vector c .. as row]] ---> so M.t is needed as needed by the Linear Alzebra transformation

from spglib: \mathbf{x} = (\mathbf{a}, \mathbf{b}, \mathbf{c}) oldsymbol{x}.

( \mathbf{a}_\mathrm{p} \; \mathbf{b}_\mathrm{p} \; \mathbf{c}_\mathrm{p} )
    = ( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \;
    \mathbf{c}_\mathrm{s} )  oldsymbol{P}_\mathrm{c},

Below is from AI: may be wrong!!

if M and cell_matrix are column major

Transform Cell Vectors(Swap \(a,b,c o c,a,b\)) np.dot(M, cell_matrix) \(M\) acts on the columns of cell_matrix from the left, shuffling the vectors.

Transform Fractional Atoms np.dot(np.linalg.inv(M), atom_coord) Coordinates change by the inverse (If single atom is a column [3, 1]) transformation to keep the physical position invariant.

If both row major:

                                          np.dot(cell_matrix, M.T)    Multiplying by $M^T$ on the right acts on the rows of
                                                                      cell_matrix, swapping vector positions

(Array of atoms [N, 3]) np.dot(direct_coords, M) ..

`apply_basis_rotation(M)` ¶

Apply any 3x3 transformation matrix to the cell and atomic positions. Assumes M and cell_matrix are in Row-Major format, and atm_position is a numpy array of shape (N, 3).

`get_poscar()` ¶

XXXXXXXXXXXXXXXXXXXXXXXXXX---DEPRECATED-------DEPRECATED ------------------XXXXXXXXXXXXXXXXXXXXXX ** get_poscar is deprecated; use read_poscar instead!! ** read poscar file present in the current dir or in the location specified.

`get_reciprocal_lattice()` ¶

return the reciprocal lattice vectors
input: real space lattice vectors: LV1, LV2, LV3 output: reciprocal space lattice vectors: b1, b2, b3 - note: a factor of 2pi is included in b1, b2, and b3

`reciprocal_lattice()` ¶

deprecated: method to calculate the reciprocal lattice vectors

`get_all_atoms_labels()` ¶

by reading POSCAR, find the atomic labels of the atoms and total no of atoms

Parameters:

string: POSCAR file in current dir.

Return:

list : strings of atomic lebels of all atoms according to the numbering of atoms in POSCAR file
scalar: total number of atoms in the POSCAR file
list:  integer numbers starting from 1 to ntotal for all atoms(e.g. 1 1 1 2 3 4 4 ..)

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

`__each_atm_type()` ¶

by reading POSCAR, label each atoms of same type with same integer

parameters

input: POSCAR file in current dir. poscar file

Returns:

list ( list of integer numbers starting from 1 to ntotal for all atoms(e.g. 1 1 1 2 3 4 4 ..) ) –

`get_unique_list(inp)` ¶

get unique elements of list

return: string 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

return:

  list of integers for each type of atoms specifying their number

`write_poscar_(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False)` ¶

create POSCAR file given the cell_parameters, atomic postions, and atom labels. Optionally the name of output POSCAR can be provided. When dealing with mutliple POSCAR file, better to provide the name of the output POSCAR file.

Parameters:

latt_obj –
name_outfile (str, default: None ) –

name of the output POSCAR file
extension (str, default: None ) –

Returns:

generates POSCAR file with name = name_outfile.extension –

`write_poscar(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False)` ¶

create POSCAR file given the cell_parameters, atomic postions, and atom labels. Optionally the name of output POSCAR can be provided. When dealing with mutliple POSCAR file, better to provide the name of the output POSCAR file.

Parameters:

latt_obj –
name_outfile (str, default: None ) –

name of the output POSCAR file
extension (str, default: None ) –

Returns:

writes POSCAR file with name = name_outfile.extension –

`get_selectivePOSCAR(ldisp=True, disp_atoms_num=None, outfile=None)` ¶

get displaced poscar with selective tag and atomic positions tagged by T T T or F F F

Parameters:

ldisp –

whether fix atoms or not
disp_atoms_num –

list of atoms indices as strings; e.g: ["1-2", '3']
outfile –

output file name

Returns:

POSCAR file with selective dynamics tags –

`get_selectivePOSCAR_adv(ldisp=True, disp_atoms_num=None, fix_direction=None, coord='cartesian', outfile=None)` ¶

get displaced poscar with selective tag and atomic positions tagged by T T T or F F F

Parameters:

ldisp –

whether fix atoms or not
disp_atoms_num –

list of atoms indices as strings to be fixed during DFT relaxation; e.g: ["1-2", '3']
fix_direction –

x, y, or z direciton; by default atoms are fixed in all directions
coord –

cartesian or direct coordinates; default: cartesian
outfile –

output file name

Returns:

POSCAR file with selective dynamics tags –

`get_dispPOSCAR(ldisp=None, disp_atoms_num=None)` ¶

deprecated: use get_selectivePOSCAR

crystal_lattice_stable19072026

esta.vaspBag.inout.crystal_lattice_stable19072026 ¶

CrystalLattice ¶

to_cartesian property ¶

to_crystal property ¶

is_crystal property ¶

is_cartesian property ¶

get_rVolume property ¶

get_volume property ¶

get_cell_vectors property ¶

get_cell_matrix property ¶

cell_matrixx property ¶

get_atm_type property ¶

get_natm_type property ¶

get_each_atm_type property ¶

is_selective_dynamics property ¶

get_cell_angle property ¶

get_atm_symbol property ¶

read_poscar_adv(verbosity=None) ¶

read_poscar(verbosity=None) ¶

set_atm_position(new_positions) ¶

set_cell_matrix(new_matrix) ¶

set_atm_symbol(new_symbol) ¶

set_atm_fix_dir(indices, direction=None) ¶

apply_basis_rotation_(M) ¶

apply_basis_rotation(M) ¶

get_poscar() ¶

get_reciprocal_lattice() ¶

reciprocal_lattice() ¶

get_all_atoms_labels() ¶

__each_atm_type() ¶

get_unique_list(inp) ¶

get_grouped_list(llist) ¶

get_neach_type(inp) ¶

write_poscar_(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False) ¶

write_poscar(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False) ¶

get_selectivePOSCAR(ldisp=True, disp_atoms_num=None, outfile=None) ¶

get_selectivePOSCAR_adv(ldisp=True, disp_atoms_num=None, fix_direction=None, coord='cartesian', outfile=None) ¶

get_dispPOSCAR(ldisp=None, disp_atoms_num=None) ¶

`esta.vaspBag.inout.crystal_lattice_stable19072026` ¶

`CrystalLattice` ¶

`to_cartesian` `property` ¶

`to_crystal` `property` ¶

`is_crystal` `property` ¶

`is_cartesian` `property` ¶

`get_rVolume` `property` ¶

`get_volume` `property` ¶

`get_cell_vectors` `property` ¶

`get_cell_matrix` `property` ¶

`cell_matrixx` `property` ¶

`get_atm_type` `property` ¶

`get_natm_type` `property` ¶

`get_each_atm_type` `property` ¶

`is_selective_dynamics` `property` ¶

`get_cell_angle` `property` ¶

`get_atm_symbol` `property` ¶

`read_poscar_adv(verbosity=None)` ¶

`read_poscar(verbosity=None)` ¶

`set_atm_position(new_positions)` ¶

`set_cell_matrix(new_matrix)` ¶

`set_atm_symbol(new_symbol)` ¶

`set_atm_fix_dir(indices, direction=None)` ¶

`apply_basis_rotation_(M)` ¶

`apply_basis_rotation(M)` ¶

`get_poscar()` ¶

`get_reciprocal_lattice()` ¶

`reciprocal_lattice()` ¶

`get_all_atoms_labels()` ¶

`__each_atm_type()` ¶

`get_unique_list(inp)` ¶

`get_grouped_list(llist)` ¶

`get_neach_type(inp)` ¶

`write_poscar_(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False)` ¶

`write_poscar(latt_obj, name_outfile: str = None, extension: str = None, ldirect=False)` ¶

`get_selectivePOSCAR(ldisp=True, disp_atoms_num=None, outfile=None)` ¶

`get_selectivePOSCAR_adv(ldisp=True, disp_atoms_num=None, fix_direction=None, coord='cartesian', outfile=None)` ¶

`get_dispPOSCAR(ldisp=None, disp_atoms_num=None)` ¶