def _parse_xyz_vel(self, inputstring):
"""
Load velocities from a XYZ file.
.. note:: The steps and symbols must be set manually before calling this
import function as a consistency measure. See also comment for
:py:meth:`._parse_xyz_pos`
"""
from aiida.common.exceptions import ValidationError
from aiida.tools.data.structure import xyz_parser_iterator
from numpy import array
numsteps = self.numsteps
if numsteps == 0:
raise ValidationError('steps must be set before importing positional data')
numsites = self.numsites
if numsites == 0:
raise ValidationError('symbols must be set before importing positional data')
velocities = array(
[[list(velocity) for _, velocity in atoms] for _, _, atoms in xyz_parser_iterator(inputstring)]
)
if velocities.shape != (numsteps, numsites, 3):
raise ValueError(
'TrajectoryData.positions must have shape (s,n,3), '
'with s=number of steps={} and '
'n=number of symbols={}'.format(numsteps, numsites)
)
self.set_array('velocities', velocities)
def _parse_xyz_pos(self, inputstring):
"""
Load positions from a XYZ file.
.. note:: The steps and symbols must be set manually before calling this
import function as a consistency measure. Even though the symbols
and steps could be extracted from the XYZ file, the data present in
the XYZ file may or may not be correct and the same logic would have
to be present in the XYZ-velocities function. It was therefore
decided not to implement it at all but require it to be set
explicitly.
Usage::
from aiida.orm.nodes.data.array.trajectory import TrajectoryData
t = TrajectoryData()
# get sites and number of timesteps
t.set_array('steps', arange(ntimesteps))
t.set_array('symbols', array([site.kind for site in s.sites]))
t.importfile('some-calc/AIIDA-PROJECT-pos-1.xyz', 'xyz_pos')
"""
from aiida.common.exceptions import ValidationError
from aiida.tools.data.structure import xyz_parser_iterator
from numpy import array
numsteps = self.numsteps
if numsteps == 0:
raise ValidationError(
'steps must be set before importing positional data')
numsites = self.numsites
if numsites == 0:
raise ValidationError(
'symbols must be set before importing positional data')
positions = array([[list(position) for _, position in atoms]
for _, _, atoms in xyz_parser_iterator(inputstring)
])
if positions.shape != (numsteps, numsites, 3):
raise ValueError(
'TrajectoryData.positions must have shape (s,n,3), '
'with s=number of steps={} and '
'n=number of symbols={}'.format(numsteps, numsites))
self.set_array('positions', positions)