# This file is part of i-PI.
# i-PI Copyright (C) 2014-2015 i-PI developers
# See the "licenses" directory for full license information.
import re
from ipi.engine.atoms import Atoms
from ipi.engine.cell import Cell
from ipi.utils.units import unit_to_internal
from ipi.engine.properties import Trajectories as Traj
# Regular expressions initialization for read_xyz function
cell_unit_re = re.compile(r'cell\{([a-z]*)\}') # cell unit pattern
traj_dict = Traj().traj_dict # trajectory dictionary
traj_re = [re.compile('%s%s' % (key, r'\{[a-z]*\}'))
for key in traj_dict.keys()] # trajectory patterns
def process_units(comment, cell, qatoms, names, masses, output='objects'):
""" Converts the data in the file according to the units written in the ipi format.
"""
# Extracting trajectory units
family, unit = 'undefined', ''
is_comment_useful = filter(None, [key.search(comment.strip())
for key in traj_re])
if len(is_comment_useful) > 0:
traj = is_comment_useful[0].group()[:-1].split('{')
family, unit = traj_dict[traj[0]]['dimension'], traj[1]
# Extracting cell units
cell_unit = ''
tmp = cell_unit_re.search(comment)
# See the "licenses" directory for full license information.
import re
from ipi.utils.messages import verbosity, info
from ipi.engine.atoms import Atoms
from ipi.engine.cell import Cell
from ipi.utils.units import unit_to_internal
from ipi.engine.properties import Trajectories as Traj
__all__ = ["auto_units", "process_units"]
# Regular expressions initialization for read_xyz function
cell_unit_re = re.compile(r"cell\{([A-Za-z_]*)\}") # cell unit pattern
traj_dict = Traj().traj_dict # trajectory dictionary
traj_re = [
re.compile("%s%s" % (key, r"\{[A-Za-z_]*\}"))
for key in list(traj_dict.keys())
] # trajectory patterns
def auto_units(
comment="",
dimension="automatic",
units="automatic",
cell_units="automatic",
mode="xyz",
):
"""Processes comment line and requested units to determine how to interpret the I/O conversion."""
# heuristics to detect units
if mode in ("pdb", "ase"): # these are the default units
auto_cell = "angstrom"
auto_units = "angstrom"
"""
import sys
import re
from ipi.utils.io import read_file, print_file, read_file_raw
from ipi.utils.depend import *
from ipi.utils.units import *
from ipi.utils.io.io_units import process_units
from ipi.engine.properties import Trajectories as Traj
from ipi.utils.messages import verbosity
cell_unit_re = re.compile(r'cell\{([A-Za-z_]*)\}') # cell unit pattern
traj_dict = Traj().traj_dict # trajectory dictionary
traj_re = [re.compile('%s%s' % (key, r'\{[A-Za-z_]*\}')) for key in traj_dict.keys()] # trajectory patterns
verbosity.level = "low"
def get_cell_units(comment, mode):
# default units
if mode == "pdb":
auto_cell = "angstrom"
else:
auto_cell = "atomic_unit"
cunit = cell_unit_re.search(comment)
if cunit is not None:
auto_cell = cunit.group(1)
return auto_cell
# i-PI Copyright (C) 2014-2015 i-PI developers
# See the "licenses" directory for full license information.
import re
from ipi.utils.messages import verbosity, info, warning
from ipi.engine.atoms import Atoms
from ipi.engine.cell import Cell
from ipi.utils.units import unit_to_internal
from ipi.engine.properties import Trajectories as Traj
__all__ = ["auto_units", "process_units"]
# Regular expressions initialization for read_xyz function
cell_unit_re = re.compile(r'cell\{([A-Za-z_]*)\}') # cell unit pattern
traj_dict = Traj().traj_dict # trajectory dictionary
traj_re = [
re.compile('%s%s' % (key, r'\{[A-Za-z_]*\}')) for key in traj_dict.keys()
] # trajectory patterns
def auto_units(comment="",
dimension="automatic",
units="automatic",
cell_units="automatic",
mode="xyz"):
""" Processes comment line and requested units to determine how to interpret the I/O conversion. """\
# heuristics to detect units
if mode == "pdb": # these are the default units
auto_cell = "angstrom"
auto_units = "angstrom"
auto_dimension = "length"
# See the "licenses" directory for full license information.
import re
from ipi.utils.messages import verbosity, info, warning
from ipi.engine.atoms import Atoms
from ipi.engine.cell import Cell
from ipi.utils.units import unit_to_internal
from ipi.engine.properties import Trajectories as Traj
__all__ = ["auto_units", "process_units"]
# Regular expressions initialization for read_xyz function
cell_unit_re = re.compile(r'cell\{([A-Za-z_]*)\}') # cell unit pattern
traj_dict = Traj().traj_dict # trajectory dictionary
traj_re = [re.compile('%s%s' % (key, r'\{[A-Za-z_]*\}'))
for key in traj_dict.keys()] # trajectory patterns
def auto_units(comment="", dimension="automatic", units="automatic", cell_units="automatic", mode="xyz"):
""" Processes comment line and requested units to determine how to interpret the I/O conversion. """\
# heuristics to detect units
if mode == "pdb": # these are the default units
auto_cell = "angstrom"
auto_units = "angstrom"
auto_dimension = "length"
else:
auto_cell = "atomic_unit"
auto_units = "atomic_unit"
auto_dimension = "undefined"