"""Read and write XYZ files."""
import datetime
import numpy as np
import unyt as u
from gmso.core.atom import Atom
from gmso.core.topology import Topology
[docs]def read_xyz(filename):
"""Reader for xyz file format.
Read in an xyz file at the given path and return a Topology object.
Parameters
----------
filename : str
Path to .xyz file that need to be read.
Return
------
top : topology.Topology
Topology object
"""
top = Topology()
with open(filename, "r") as xyz_file:
n_atoms = int(xyz_file.readline())
xyz_file.readline()
coords = np.zeros(shape=(n_atoms, 3)) * u.nanometer
for row, _ in enumerate(coords):
line = xyz_file.readline().split()
if not line:
msg = (
"Incorrect number of lines in input file. Based on the "
"number in the first line of the file, {} rows of atoms "
"were expected, but at least one fewer was found."
)
raise ValueError(msg.format(n_atoms))
tmp = np.array(line[1:4], dtype=np.float) * u.angstrom
coords[row] = tmp.in_units(u.nanometer)
site = Atom(name=line[0], position=coords[row])
top.add_site(site)
top.update_topology()
# Verify we have read the last line by ensuring the next line in blank
line = xyz_file.readline().split()
if line:
msg = (
"Incorrect number of lines in input file. Based on the "
"number in the first line of the file, {} rows of atoms "
"were expected, but at least one more was found."
)
raise ValueError(msg.format(n_atoms))
return top
[docs]def write_xyz(top, filename):
"""Writer for xyz file format.
Write a Topology object to an xyz file at the given path.
Parameters
----------
top : topology.Topology
Topology object that needs to be written out.
filename : str
Path to file location.
"""
with open(filename, "w") as out_file:
out_file.write("{:d}\n".format(top.n_sites))
out_file.write(
"{} {} written by topology at {}\n".format(
top.name, filename, str(datetime.datetime.now())
)
)
for idx, site in enumerate(top.sites):
# TODO: Better handling of element guessing and site naming
if site.element is not None:
tmp_name = site.element.symbol
else:
tmp_name = "X"
out_file.write(
"{0} {1:8.3f} {2:8.3f} {3:8.3f}\n".format(
tmp_name,
site.position[0].in_units(u.angstrom).value,
site.position[1].in_units(u.angstrom).value,
site.position[2].in_units(u.angstrom).value,
)
)