def write(self, atomdict):
"""
Write an atom to the file.
Args:
atom (dict): a dictionary describing the atom.
"""
from BigDFT.Atoms import Atom
at = Atom(atomdict)
self._handle.write(at.sym + " ")
pos = at.get_position(self.units)
self._handle.write(" ".join([str(x) for x in pos]))
self._handle.write("\n")
def update_positions_from_dict(self, posinp):
"""
Update the atomic positions of a system from a posinp dictionary.
This method only works if the order of atoms match.
Args:
posinp (dict): a posinp dictionary.
"""
from BigDFT.Atoms import Atom
units = posinp.get("units", "angstroem")
i = 0
for frag in self.values():
for at in frag:
at2 = Atom(posinp["positions"][i], units=units)
at.set_position(at2.get_position())
i += 1