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# fmt: off
"""
Use lammpsdata module to create an Atoms object from a lammps data file
and checks that the cell, mass, positions, and velocities match the
values that are parsed directly from the data file.
NOTE: This test currently only works when using a lammps data file
containing a single atomic species
"""
import ase.io
from .comparison import compare_with_pytest_approx
from .parse_lammps_data_file import lammpsdata_file_extracted_sections
# Relative tolerance for comparing floats with pytest.approx
REL_TOL = 1e-2
def test_lammpsdata_read(lammpsdata_file_path):
atoms = ase.io.read(
lammpsdata_file_path,
format='lammps-data',
read_image_flags=False,
units='metal',
)
expected_values = lammpsdata_file_extracted_sections(lammpsdata_file_path)
# Check cell was read in correctly
cell_read_in = atoms.get_cell()
cell_expected = expected_values['cell']
compare_with_pytest_approx(cell_read_in, cell_expected, REL_TOL)
# Check masses were read in correctly
masses_read_in = atoms.get_masses()
masses_expected = [expected_values['mass']] * \
len(expected_values['positions'])
compare_with_pytest_approx(masses_read_in, masses_expected, REL_TOL)
# Check positions were read in correctly
positions_read_in = atoms.get_positions()
positions_expected = expected_values['positions']
compare_with_pytest_approx(positions_read_in, positions_expected, REL_TOL)
# Check velocities were read in correctly
velocities_read_in = atoms.get_velocities()
velocities_expected = expected_values['velocities']
compare_with_pytest_approx(velocities_read_in, velocities_expected, REL_TOL)
# TODO: Also check charges, travels, molecule id, bonds, and angles
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