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Use get_atomic_numbers instead of atomic_numbers #22

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Merged
merged 6 commits into from
May 25, 2023
Merged

Use get_atomic_numbers instead of atomic_numbers #22

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28c52db
Add `parent` to `get_chemical_symbols`
samwaseda May 24, 2023
59b0fe0
use ASE-native get_atomic_numbers
samwaseda May 25, 2023
faf48d9
remove get_atomic_numbers
samwaseda May 25, 2023
bb9c71a
replace get_atomic_numbers by structure.get_atomic_numbers
samwaseda May 25, 2023
111c1d3
remove from __init__.py
samwaseda May 25, 2023
51d9d6d
Update __init__.py
jan-janssen May 25, 2023
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1 change: 0 additions & 1 deletion structuretoolkit/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,6 @@
ase_to_pymatgen,
ase_to_pyscal,
center_coordinates_in_unit_cell,
get_atomic_numbers,
get_extended_positions,
get_vertical_length,
get_wrapped_coordinates,
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1 change: 0 additions & 1 deletion structuretoolkit/common/__init__.py
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Expand Up @@ -2,7 +2,6 @@
from structuretoolkit.common.helper import (
apply_strain,
center_coordinates_in_unit_cell,
get_atomic_numbers,
get_extended_positions,
get_vertical_length,
get_wrapped_coordinates,
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4 changes: 0 additions & 4 deletions structuretoolkit/common/helper.py
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Expand Up @@ -3,10 +3,6 @@
from scipy.sparse import coo_matrix


def get_atomic_numbers(structure):
return [atomic_numbers[el] for el in structure.get_chemical_symbols()]


def get_extended_positions(
structure, width, return_indices=False, norm_order=2, positions=None
):
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6 changes: 2 additions & 4 deletions structuretoolkit/visualize.py
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Expand Up @@ -7,8 +7,6 @@
import numpy as np
from scipy.interpolate import interp1d

from structuretoolkit.common.helper import get_atomic_numbers

__author__ = "Joerg Neugebauer, Sudarsan Surendralal"
__copyright__ = (
"Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
Expand Down Expand Up @@ -184,7 +182,7 @@ def _plot3d_plotly(
if select_atoms is None:
select_atoms = np.arange(len(structure))
elements = structure.get_chemical_symbols()
atomic_numbers = get_atomic_numbers(structure=structure)
atomic_numbers = structure.get_atomic_numbers()
if scalar_field is None:
scalar_field = elements
fig = px.scatter_3d(
Expand Down Expand Up @@ -302,7 +300,7 @@ def _plot3d(
vector_field = structure.get_initial_magnetic_moments()

elements = structure.get_chemical_symbols()
atomic_numbers = get_atomic_numbers(structure=structure)
atomic_numbers = structure.get_atomic_numbers()
positions = structure.positions

# If `select_atoms` was given, visualize only a subset of the `parent_basis`
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