# Copyright (c) 2020 The Regents of the University of Michigan
# All rights reserved.
# This software is licensed under the BSD 3-Clause License.
"""cif-file writer for the Glotzer Group, University of Michigan.
Authors: Julia Dshemuchadse, Carl Simon Adorf
.. code::
writer = CifFileWriter()
# write to screen:
write.write(trajectory)
# write to file:
with open('a_ciffile.pos', 'w') as ciffile:
writer.write(trajectory, ciffile)
"""
import io
import sys
import logging
import math
import datetime
from collections import defaultdict
import numpy as np
logger = logging.getLogger(__name__)
def _determine_unitcell(box):
lengths = np.sqrt(np.sum(np.array(box.get_box_matrix())**2, axis=0)) # a, b, c
gamma = math.degrees(
np.arccos(
box.xy / math.sqrt(1 + box.xy ** 2)))
beta = math.degrees(
np.arccos(
box.xz / math.sqrt(1 + box.xz ** 2 + box.yz ** 2)))
alpha = math.degrees(
np.arccos(
(box.xy * box.xz + box.yz) /
(math.sqrt(1 + box.xy ** 2)
* math.sqrt(1 + box.xz ** 2 + box.yz ** 2))))
angles = np.array([alpha, beta, gamma])
return lengths, angles
[docs]class CifFileWriter(object):
"""cif-file writer for the Glotzer Group, University of Michigan.
Authors: Julia Dshemuchadse, Carl Simon Adorf
.. code::
writer = CifFileWriter()
# write to screen:
write.write(trajectory)
# write to file:
with open('a_ciffile.pos', 'w') as ciffile:
writer.write(trajectory, ciffile)
"""
def _write_frame(self, frame, file, data, occupancies, fractional, raw):
from . import __version__
if occupancies is None:
occupancies = np.ones(frame.position.shape[0])
def _write(msg='', end='\n'):
file.write(msg + end)
unitcell_lengths, unitcell_angles = _determine_unitcell(frame.box)
# write title
_write("data_" + data)
# _write("data_" + os.path.splitext(ciffilename)[0])
_write("_audit_creation_method "
"'generated by garnett {}'".format(__version__))
_write("_audit_creation_date {}".format(str(datetime.date.today())))
# write unit cell parameters
_write("_cell_length_a {}".format(unitcell_lengths[0]))
_write("_cell_length_b {}".format(unitcell_lengths[1]))
_write("_cell_length_c {}".format(unitcell_lengths[2]))
_write("_cell_angle_alpha {}".format(unitcell_angles[0]))
_write("_cell_angle_beta {}".format(unitcell_angles[1]))
_write("_cell_angle_gamma {}".format(unitcell_angles[2]))
_write()
# write symmetry - P1
_write("_symmetry_space_group_name_H-M " + "'P 1'")
_write("_symmetry_Int_Tables_number " + str(1))
_write()
# write header for particle positions
_write("loop_")
_write("_atom_site_label")
_write("_atom_site_type_symbol")
_write("_atom_site_occupancy")
_write("_atom_site_fract_x")
_write("_atom_site_fract_y")
_write("_atom_site_fract_z")
# write header particle positions
if raw:
fractions = frame.cif_coordinates.copy()
else:
if fractional:
fractions = frame.position.copy()
else:
invbox = np.linalg.inv(frame.box.get_box_matrix())
fractions = np.dot(invbox, frame.position.T).T
fractions += 0.5
type_counter = defaultdict(int)
n_digits = len(str(len(frame.position)))
particle_str = "{ptype}{pnum:0" + str(n_digits) + "d} {ptype} {occ:3.2f} {position}"
for i, (position, typeid, occupancy) in enumerate(zip(fractions, frame.typeid, occupancies)):
particle_type = frame.types[typeid]
_write(particle_str.format(
pnum=type_counter[particle_type],
ptype=particle_type,
occ=occupancy,
position=' '.join(map(str, position))))
type_counter[particle_type] += 1
[docs] def write(self, trajectory, file=sys.stdout,
data='simulation', occupancy=None, fractional=False, raw=False):
"""Serialize a trajectory into cif-format and write it to file.
:param trajectory: The trajectory to serialize
:type trajectory: :class:`~garnett.trajectory.Trajectory`
:param file: The file to write the trajectory to.
:type file: A file-like object.
:param data: Identifier which be will written to the file,
signifying the origin of the data.
:type data: str
:param occupancy: The default occupancy of individual particles.
:type occupancy: int
:param fractional: Whether or not the input coordinates are fractional
:type fractional: bool
:param raw: Whether or not to write the raw CIF coordinates (with no transformations)
:type raw: bool
"""
for i, frame in enumerate(trajectory):
self._write_frame(
frame=frame,
file=file,
data='{}_frame_{}'.format(data, i),
occupancies=occupancy,
fractional=fractional,
raw=raw)
logger.debug("Wrote frame {}.".format(i + 1))
logger.info("Wrote {} frames.".format(i + 1))
[docs] def dump(self, trajectory, data='simulation', occupancy=None,
fractional=False, raw=False):
"""Serialize trajectory into cif-format.
:param trajectory: The trajectory to serialize.
:type trajectory: :class:`~garnett.trajectory.Trajectory`
:param data: Identifier which be will written to the file,
signifying the origin of the data.
:type data: str
:param occupancy: The default occupancy of individual particles.
:type occupancy: numpy.array
:rtype: str
"""
f = io.StringIO()
self.write(trajectory, f, occupancy=occupancy, fractional=fractional, raw=raw)
return f.getvalue()