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"""
Routines for manually parsing a lammps data file. This is a simplified
recreation of ase.io.lammpsdata's read functionality that we use for
testing so as to attempt to provide an independent verification. It is
fairly ad hoc and was designed specifically to work for the
'lammpsdata_input.data' file under ase.test.testdata. In particular,
the following assumptions are made about the lammps data file:
- Only a single atomic species is present
- The cell is orthogonal (xy, xz, yz tilt factors are
ignored even if they exist)
"""
import io
import re
import pathlib
import numpy as np
from ase.calculators.lammps import convert
def split_contents_by_section(raw_datafile_contents):
return re.split(r"^([A-Za-z]+\s*)$\n", raw_datafile_contents, flags=re.MULTILINE)
def extract_section(raw_datafile_contents, section_header):
contents_split_by_section = split_contents_by_section(raw_datafile_contents)
section = None
for ind, block in enumerate(contents_split_by_section):
if block.startswith(section_header):
section = contents_split_by_section[ind + 1].strip()
break
return section
def extract_cell(raw_datafile_contents):
"""
NOTE: Assumes an orthogonal cell (xy, xz, yz tilt factors are
ignored even if they exist)
"""
RE_CELL = re.compile(
r"""
(\S+)\s+(\S+)\s+xlo\s+xhi\n
(\S+)\s+(\S+)\s+ylo\s+yhi\n
(\S+)\s+(\S+)\s+zlo\s+zhi\n
""",
flags=re.VERBOSE,
)
xlo, xhi, ylo, yhi, zlo, zhi = map(
float, RE_CELL.search(raw_datafile_contents).groups()
)
cell = [[xhi - xlo, 0, 0], [0, yhi - ylo, 0], [0, 0, zhi - zlo]]
return cell
def extract_mass(raw_datafile_contents):
"""
NOTE: Assumes that only a single atomic species is present
"""
masses_block = extract_section(raw_datafile_contents, "Masses")
if masses_block is None:
return None
else:
mass = re.match(r"\s*[0-9]+\s+(\S+)", masses_block).group(1)
return float(mass)
def extract_atom_quantities(raw_datafile_contents):
# Grab all atoms lines
atoms_block = extract_section(raw_datafile_contents, "Atoms")
# Now parse each individual atoms line for quantities
charges = []
positions = []
travels = []
RE_ATOM_LINE = re.compile(
r"\s*[0-9]+\s+[0-9]+\s+[0-9]+\s+(\S+)\s+"
r"(\S+)\s+(\S+)\s+(\S+)\s?"
r"([0-9-]+)?\s?([0-9-]+)?\s?([0-9-]+)?"
)
for atom_line in atoms_block.splitlines():
q, x, y, z, *travel = RE_ATOM_LINE.match(atom_line).groups()
charges.append(float(q))
positions.append(list(map(float, [x, y, z])))
if None not in travel:
travels.append(list(map(int, travel)))
else:
travels.append(None)
return charges, positions, travels
def extract_velocities(raw_datafile_contents):
"""
NOTE: Assumes metal units are used in data file
"""
velocities_block = extract_section(raw_datafile_contents, "Velocities")
RE_VELOCITY = re.compile(
r"\s*[0-9]+\s+(\S+)\s+(\S+)\s+(\S+)"
)
# Now parse each individual line for velocity
velocities = []
for velocities_line in velocities_block.splitlines():
v = RE_VELOCITY.match(velocities_line).groups()
velocities.append(list(map(float, v)))
# Convert to ASE's velocity units (uses unusual unit of time)
velocities = convert(np.asarray(velocities), "velocity", "metal", "ASE")
return velocities
def lammpsdata_file_extracted_sections(lammpsdata):
"""
Manually read a lammpsdata file and grep for the different
quantities we want to check. Accepts either a string indicating the name
of the file, a pathlib.Path object indicating the location of the file, a
StringIO object containing the file contents, or a file object
"""
if isinstance(lammpsdata, str) or isinstance(lammpsdata, pathlib.Path):
with open(lammpsdata) as fd:
raw_datafile_contents = fd.read()
elif isinstance(lammpsdata, io.StringIO):
raw_datafile_contents = lammpsdata.getvalue()
elif isinstance(lammpsdata, io.TextIOBase):
raw_datafile_contents = lammpsdata.read()
else:
raise ValueError(
"Lammps data file content inputted in unsupported "
"object type {type(lammpsdata)}"
)
cell = extract_cell(raw_datafile_contents)
mass = extract_mass(raw_datafile_contents)
charges, positions, travels = extract_atom_quantities(raw_datafile_contents)
velocities = extract_velocities(raw_datafile_contents)
return {
"cell": cell,
"mass": mass,
"charges": charges,
"positions": positions,
"travels": travels,
"velocities": velocities,
}
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