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# fmt: off
"""Test write and read."""
import io
import re
import numpy as np
import pytest
from ase import Atoms
from ase.build import bulk
from ase.data import atomic_numbers
from ase.io.lammpsdata import read_lammps_data, write_lammps_data
def compare(atoms: Atoms, atoms_ref: Atoms):
"""Compare two `Atoms` objects"""
assert all(atoms.numbers == atoms_ref.numbers)
assert atoms.get_masses() == pytest.approx(atoms_ref.get_masses())
# Note: Raw positions cannot be compared.
# `write_lammps_data` changes cell orientation.
assert atoms.get_scaled_positions() == pytest.approx(
atoms_ref.get_scaled_positions())
@pytest.mark.parametrize('masses', [False, True])
class _Base:
def run(self, atoms_ref: Atoms, masses: bool):
"""Run tests"""
self.check_explicit_numbers(atoms_ref, masses)
if masses:
self.check_masses2numbers(atoms_ref)
def check_explicit_numbers(self, atoms_ref: Atoms, masses: bool):
"""Check if write-read is consistent when giving Z_of_type."""
buf = io.StringIO()
write_lammps_data(buf, atoms_ref, masses=masses)
buf.seek(0)
# By default, write_lammps_data assigns atom types to the elements in
# alphabetical order. To be consistent, here spiecies are also sorted.
species = sorted(set(atoms_ref.get_chemical_symbols()))
Z_of_type = {i + 1: atomic_numbers[s] for i, s in enumerate(species)}
atoms = read_lammps_data(buf, Z_of_type=Z_of_type, atom_style='atomic')
compare(atoms, atoms_ref)
def check_masses2numbers(self, atoms_ref: Atoms):
"""Check if write-read is consistent when guessing atomic numbers."""
buf = io.StringIO()
write_lammps_data(buf, atoms_ref, masses=True)
buf.seek(0)
atoms = read_lammps_data(buf, atom_style='atomic')
compare(atoms, atoms_ref)
@pytest.mark.parametrize('cubic', [False, True])
class TestCubic(_Base):
"""Test cubic structures."""
def test_bcc(self, cubic: bool, masses: bool):
"""Test bcc."""
atoms_ref = bulk('Li', 'bcc', cubic=cubic)
self.run(atoms_ref, masses)
def test_fcc(self, cubic: bool, masses: bool):
"""Test fcc."""
atoms_ref = bulk('Cu', 'fcc', cubic=cubic)
self.run(atoms_ref, masses)
def test_rocksalt(self, cubic: bool, masses: bool):
"""Test rocksalt."""
atoms_ref = bulk('NaCl', 'rocksalt', a=1.0, cubic=cubic)
self.run(atoms_ref, masses)
def test_fluorite(self, cubic: bool, masses: bool):
"""Test fluorite."""
atoms_ref = bulk('CaF2', 'fluorite', a=1.0, cubic=cubic)
self.run(atoms_ref, masses)
@pytest.mark.parametrize('orthorhombic', [False, True])
class TestOrthorhombic(_Base):
"""Test orthorhombic structures."""
def test_hcp(self, orthorhombic: bool, masses: bool):
"""Test hcp."""
atoms_ref = bulk('Mg', 'hcp', orthorhombic=orthorhombic)
self.run(atoms_ref, masses)
@pytest.mark.parametrize('atom_style', ['atomic', 'charge', 'full'])
def test_atom_style(atom_style: str):
"""Test `atom_style`"""
atoms_ref = bulk('Cu', 'fcc')
# note that we should do `masses=True` to later guess atomic numbers
buf = io.StringIO()
write_lammps_data(buf, atoms_ref, masses=True, atom_style=atom_style)
# test if the `atom_style` can be guessed from the comment
buf.seek(0)
atoms = read_lammps_data(buf, atom_style=None)
compare(atoms, atoms_ref)
# test when `atom_style` is explicitly specified
buf.seek(0)
atoms = read_lammps_data(buf, atom_style=atom_style)
compare(atoms, atoms_ref)
if atom_style not in ['atomic', 'full']:
return
# test if `atom_style` can be guessed from the length of fields
# remove comment in the 'Atoms' line
buf = io.StringIO(re.sub('.*Atoms.*#.*', 'Atoms', buf.getvalue()))
atoms = read_lammps_data(buf, atom_style=None)
compare(atoms, atoms_ref)
@pytest.mark.parametrize('atom_style', ['atomic', 'charge', 'full'])
@pytest.mark.parametrize('write_image_flags', [False, True])
def test_image_flags(write_image_flags: bool, atom_style: str):
"""Test if `wrap` and `write_image_flags` work correctly."""
atoms_ref = bulk('Ge')
# shift atomic positions
scaled_positions = atoms_ref.get_scaled_positions(wrap=False)
shift = (0.125, 1.125, -0.125)
atoms_ref.set_scaled_positions(scaled_positions + shift)
# note that we should do `masses=True` to later guess atomic numbers
buf = io.StringIO()
write_lammps_data(
buf,
atoms_ref,
write_image_flags=write_image_flags,
masses=True,
atom_style=atom_style,
)
buf.seek(0)
atoms = read_lammps_data(buf)
# The atomic positions should be wrapped.
np.testing.assert_allclose(
atoms.get_scaled_positions(wrap=False),
atoms_ref.get_scaled_positions(wrap=False),
)
def test_bonds(lammpsdata_file_path):
"""Test if writing bonds works correctly."""
atoms = read_lammps_data(lammpsdata_file_path, atom_style='full')
lammpsdata_buf = io.StringIO()
write_lammps_data(
lammpsdata_buf, atoms, atom_style='full',
masses=True, velocities=True, bonds=True)
lammpsdata_buf.seek(0)
atoms2 = read_lammps_data(lammpsdata_buf, atom_style='full')
np.testing.assert_array_equal(
atoms.arrays["bonds"], atoms2.arrays["bonds"]
)
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