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# fmt: off
"""SiestaInput"""
import warnings
import numpy as np
from ase import Atoms
from ase.constraints import FixAtoms, FixCartesian, FixedLine, FixedPlane
class SiestaInput:
"""SiestaInput"""
@classmethod
def is_along_cartesian(cls, norm_dir: np.ndarray) -> bool:
"""Return whether `norm_dir` is along a Cartesian coordidate."""
directions = [
[+1, 0, 0],
[-1, 0, 0],
[0, +1, 0],
[0, -1, 0],
[0, 0, +1],
[0, 0, -1],
]
for direction in directions:
if np.allclose(norm_dir, direction, rtol=0.0, atol=1e-6):
return True
return False
@classmethod
def generate_kpts(cls, kpts):
"""Write kpts.
Parameters:
- f : Open filename.
"""
yield '\n'
yield '#KPoint grid\n'
yield '%block kgrid_Monkhorst_Pack\n'
for i in range(3):
s = ''
if i < len(kpts):
number = kpts[i]
displace = 0.0
else:
number = 1
displace = 0
for j in range(3):
if j == i:
write_this = number
else:
write_this = 0
s += f' {write_this:d} '
s += f'{displace:1.1f}\n'
yield s
yield '%endblock kgrid_Monkhorst_Pack\n'
yield '\n'
@classmethod
def get_species(cls, atoms, species, basis_set):
from ase.calculators.siesta.parameters import Species
# For each element use default species from the species input, or set
# up a default species from the general default parameters.
tags = atoms.get_tags()
default_species = [
s for s in species
if (s['tag'] is None) and s['symbol'] in atoms.symbols]
default_symbols = [s['symbol'] for s in default_species]
for symbol in atoms.symbols:
if symbol not in default_symbols:
spec = Species(symbol=symbol,
basis_set=basis_set,
tag=None)
default_species.append(spec)
default_symbols.append(symbol)
assert len(default_species) == len(set(atoms.symbols))
# Set default species as the first species.
species_numbers = np.zeros(len(atoms), int)
i = 1
for spec in default_species:
mask = atoms.symbols == spec['symbol']
species_numbers[mask] = i
i += 1
# Set up the non-default species.
non_default_species = [s for s in species if s['tag'] is not None]
for spec in non_default_species:
mask1 = tags == spec['tag']
mask2 = atoms.symbols == spec['symbol']
mask = np.logical_and(mask1, mask2)
if sum(mask) > 0:
species_numbers[mask] = i
i += 1
all_species = default_species + non_default_species
return all_species, species_numbers
@classmethod
def make_xyz_constraints(cls, atoms: Atoms):
""" Create coordinate-resolved list of constraints [natoms, 0:3]
The elements of the list must be integers 0 or 1
1 -- means that the coordinate will be updated during relaxation
0 -- mains that the coordinate will be fixed during relaxation
"""
moved = np.ones((len(atoms), 3), dtype=int) # (0: fixed, 1: updated)
for const in atoms.constraints:
if isinstance(const, FixAtoms):
moved[const.get_indices()] = 0
elif isinstance(const, FixedLine):
norm_dir = const.dir / np.linalg.norm(const.dir)
if not cls.is_along_cartesian(norm_dir):
raise RuntimeError(
f'norm_dir {norm_dir} is not one of the Cartesian axes'
)
norm_dir = norm_dir.round().astype(int)
moved[const.get_indices()] = norm_dir
elif isinstance(const, FixedPlane):
norm_dir = const.dir / np.linalg.norm(const.dir)
if not cls.is_along_cartesian(norm_dir):
raise RuntimeError(
f'norm_dir {norm_dir} is not one of the Cartesian axes'
)
norm_dir = norm_dir.round().astype(int)
moved[const.get_indices()] = abs(1 - norm_dir)
elif isinstance(const, FixCartesian):
moved[const.get_indices()] = 1 - const.mask.astype(int)
else:
warnings.warn(f'Constraint {const!s} is ignored')
return moved
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