################################################################################
# Copyright (c), AiiDA team and individual contributors. #
# All rights reserved. #
# This file is part of the AiiDA-wannier90 code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-wannier90 #
# For further information on the license, see the LICENSE.txt file #
################################################################################
"""Write input to a ``.win`` file."""
import copy
import typing as ty
from aiida import orm
from aiida.common import InputValidationError
from ..utils import conv_to_fortran_withlists
from ._group_list import list_to_grouped_string
__all__ = ("write_win",)
[docs]def write_win( # pylint: disable=too-many-arguments
filename,
parameters,
kpoints=None,
structure=None,
kpoint_path=None,
bands_kpoints=None,
projections=None,
random_projections=False,
):
"""Write input to a ``.win`` file.
:param filename: Path of the file where the input is written.
:type filename: str
:param parameters: Additional input parameters, as specified in the Wannier90 user guide.
:type parameters: dict, aiida.orm.nodes.data.dict.Dict
:param structure: Structure of the calculated material.
:type structure: aiida.orm.nodes.data.structure.StructureData
:param kpoints: Mesh of k-points used for the Wannierization procedure.
:type kpoints: aiida.orm.nodes.data.array.kpoints.KpointsData
:param kpoint_path: List of k-points used for band interpolation.
:type kpoint_path: aiida.orm.nodes.data.dict.Dict
:param bands_kpoints: An explicit list of k-points used for band interpolation.
:type bands_kpoints: aiida.orm.KpointsData
:param projections: Orbitals used for the projections. Can be specified either as AiiDA class
:py:class:`OrbitalData <aiida.orm.OrbitalData>`,
or as a list of strings specifying the projections in Wannier90's format.
:type projections: aiida.orm.nodes.data.orbital.OrbitalData, aiida.orm.nodes.data.list.List[str]
:param random_projections: If class :py:class:`OrbitalData <aiida.orm.OrbitalData>` is used for projections,
enables random projections completion
:type random_projections: aiida.orm.nodes.data.bool.Bool
"""
with open(filename, "w", encoding="utf-8") as file:
file.write(
_create_win_string(
parameters=parameters,
structure=structure,
kpoints=kpoints,
kpoint_path=kpoint_path,
bands_kpoints=bands_kpoints,
projections=projections,
random_projections=random_projections,
)
)
def _create_win_string( # pylint: disable=too-many-arguments
parameters,
kpoints,
structure=None,
kpoint_path=None,
bands_kpoints=None,
projections=None,
random_projections=False,
):
"""Generate a string with the content of a .win file."""
from aiida.orm import List
from aiida.plugins import DataFactory
# prepare the main input text
input_file_lines = []
if isinstance(parameters, DataFactory("core.dict")):
parameters = parameters.get_dict()
try:
parameters.setdefault("mp_grid", kpoints.get_kpoints_mesh()[0])
except AttributeError:
pass
input_file_lines += _format_parameters(parameters)
block_inputs = {}
if projections is None:
# If no projections are specified, random projections is used (Dangerous!)
if random_projections:
block_inputs["projections"] = ["random"]
else:
block_inputs["projections"] = []
elif isinstance(projections, (tuple, list)):
if random_projections:
raise InputValidationError(
"random_projections cannot be True with (tuple,list) projections."
'Instead, use "random" string as first element of the list.'
)
block_inputs["projections"] = projections
elif isinstance(projections, List):
if random_projections:
raise InputValidationError(
"random_projections cannot be True if with List-type projections."
'Instead, use "random" string as first element of the List.'
)
block_inputs["projections"] = projections.get_list()
else:
block_inputs["projections"] = _format_all_projections(
projections, random_projections=True
)
if structure is not None:
block_inputs["unit_cell_cart"] = _format_unit_cell(structure)
block_inputs["atoms_cart"] = _format_atoms_cart(structure)
if kpoints is not None:
block_inputs["kpoints"] = _format_kpoints(kpoints)
if kpoint_path is not None:
block_inputs["kpoint_path"] = _format_kpoint_path(kpoint_path)
elif bands_kpoints is not None:
kpath, labels = _format_explicit_kpoint_path(bands_kpoints)
block_inputs["explicit_kpath"] = kpath
block_inputs["explicit_kpath_labels"] = labels
input_file_lines += _format_block_inputs(block_inputs)
return "\n".join(input_file_lines) + "\n"
def _format_parameters(parameters_dict):
"""Join key / value pairs of the parameters dictionary into formatted strings.
Returning a list of lines for the .win file.
"""
lines = []
for key, value in sorted(_format_parameter_values(parameters_dict).items()):
lines.append(key + " = " + value)
return lines
def _format_parameter_values(parameters_dict):
"""Turn the values of the parameters dictionary into the appropriate string."""
result_dict = {}
for key, value in parameters_dict.items():
key = key.lower()
if key == "exclude_bands":
if len(set(value)) < len(value):
raise InputValidationError(
"The 'exclude_bands' input contains duplicate entries."
)
if any(val <= 0 for val in value):
raise InputValidationError(
"The 'exclude_bands' values must be positive."
)
result_dict[key] = list_to_grouped_string(value)
else:
result_dict[key] = conv_to_fortran_withlists(value, quote_strings=False)
return result_dict
def _format_all_projections(projections, random_projections=False):
"""Return a list of strings, they are the lines to insert into Wannier90 projections block.
:param projections: OrbitalData object with projections info
:param random_projections: if True, add the 'random' keyword on top.
It asks the code to fill missing projections with random orbitals (see Wannier90 docs)
"""
projection_list = projections.get_orbitals()
# TODO: Check if spinor_projections actually needs to be used.
# spin_use = any([bool(projection.get_orbital_dict()['spin'])
# for projection in projection_list])
# projector_type = "spinor_projections" if spin_use else "projections"
projection_lines = [
_format_single_projection(projection) for projection in projection_list
]
if random_projections:
projection_lines = ["random"] + projection_lines
return projection_lines
def _format_single_projection(orbital): # pylint: disable=too-many-locals
"""Create an appropriate wannier line from input orbitaldata.
Will raise an exception if the orbital does not contain enough information,
or the information is badly formatted.
"""
from aiida.plugins import OrbitalFactory
RealhydrogenOrbital = OrbitalFactory("core.realhydrogen")
if not isinstance(orbital, RealhydrogenOrbital):
raise InputValidationError(
"Only realhydrogen orbitals are currently supported for Wannier90 input."
)
orb_dict = copy.deepcopy(orbital.get_orbital_dict())
def _get_attribute(name, required=True):
res = orb_dict.get(name, None)
if res is None and required:
raise InputValidationError(f"Orbital is missing attribute '{name}'.")
return res
def _format_projection_values_float(name, value):
"""Return a string for a given key-value pair of the projections block.
E.g.
``'c=0.132443,1.324823823,0.547423243'``, where we know that values are floats
that will be formatted with a specific formatting option.
"""
if value is None:
return ""
if not isinstance(value, (tuple, list)):
value = [value]
return f'{name}={",".join(f"{x:.10f}" for x in value)}'
def _format_projection_values_generic(name, value):
"""Return a string for a given key-value pair of the projections block.
E.g.
``'l=1'``, where formatting of the values is done without specifying
a custom format - this is ok for e.g. integers, while for floats it's
better to use :func:`_format_projection_values_float` function that
properly formats floats, avoiding differences between python versions.
"""
if value is None:
return ""
if not isinstance(value, (tuple, list)):
value = [value]
return f'{name}={",".join(f"{x}" for x in value)}'
# required arguments
position = _get_attribute("position")
angular_momentum = _get_attribute("angular_momentum")
magnetic_number = _get_attribute("magnetic_number")
wann_string = (
_format_projection_values_float("c", position)
+ ":"
+ _format_projection_values_generic("l", angular_momentum)
+ ","
+ _format_projection_values_generic("mr", magnetic_number + 1)
)
# optional, colon-separated arguments
zaxis = _get_attribute("z_orientation", required=False)
xaxis = _get_attribute("x_orientation", required=False)
radial = _get_attribute("radial_nodes", required=False)
zona = _get_attribute("diffusivity", required=False)
if any(arg is not None for arg in [zaxis, xaxis, radial, zona]):
zaxis_string = _format_projection_values_float("z", zaxis)
xaxis_string = _format_projection_values_float("x", xaxis)
radial_string = _format_projection_values_generic("r", radial + 1)
zona_string = _format_projection_values_float("zona", zona)
wann_string += f":{zaxis_string}:{xaxis_string}:{radial_string}:{zona_string}"
# spin, optional
# Careful with spin, it is insufficient to set the spin the projection
# line alone. You must, in addition, apply the appropriate settings:
# either set spinors=.true. or use spinor_projections, see user guide
spin = _get_attribute("spin", required=False)
if spin is not None and spin != 0:
spin_dict = {-1: "d", 1: "u"}
wann_string += f"({spin_dict[spin]})"
spin_orient = _get_attribute("spin_orientation", required=False)
if spin_orient is not None:
wann_string += "[" + ",".join([f"{x:18.10f}" for x in spin_orient]) + "]"
return wann_string
def _format_unit_cell(structure):
return ["ang"] + [
f"{vector[0]:18.10f} {vector[1]:18.10f} {vector[2]:18.10f}"
for vector in structure.cell
]
def _format_atoms_cart(structure):
"""Generate site locations and cell dimensions that can be used by the wannier90 input script."""
def list2str(list_item):
"""Convert an input list item into a str."""
list_item = copy.deepcopy(list_item)
if isinstance(list_item, str):
return list_item
return " " + " ".join([f"{_:18.10f}" for _ in list_item]) + " "
return ["ang"] + [
f"{site.kind_name} {list2str(site.position)}" for site in structure.sites
]
def _format_kpoints(kpoints):
# KpointsData was set with set_kpoints_mesh
try:
all_kpoints = kpoints.get_kpoints_mesh(print_list=True)
# KpointsData was set with set_kpoints
except AttributeError:
all_kpoints = kpoints.get_kpoints()
return [f"{k[0]:18.10f} {k[1]:18.10f} {k[2]:18.10f}" for k in all_kpoints]
def _format_kpoint_path(kpoint_path):
"""Prepare the lines for the Wannier90 input file related to the kpoint_path.
:param kpoint_path: a ParameterData containing two entries:
a 'path' list with the labels of the endpoints of each
path segment, and a dictionary called "point_coords" that gives the
three (fractional) coordinates for each label.
:return: a list of strings to be added to the input file, within the
kpoint_info block
"""
kinfo = kpoint_path.get_dict()
path = kinfo.pop("path")
point_coords = kinfo.pop("point_coords")
# In Wannier90 (from the user guide): Values are in
# fractional coordinates with respect to the primitive
# reciprocal lattice vectors.
res = []
for point1, point2 in path:
coord1 = point_coords[point1]
coord2 = point_coords[point2]
path_line = f"{point1} {coord1[0]} {coord1[1]} {coord1[2]} "
path_line += f" {point2} {coord2[0]} {coord2[1]} {coord2[2]}"
res.append(path_line)
return res
def _format_explicit_kpoint_path(bands_kpoints: orm.KpointsData) -> ty.Tuple:
"""Prepare the lines for the Wannier90 input file related to the `explicit_kpath` and `explicit_kpath_labels`.
:param bands_kpoints: a KpointsData which must contain labels.
:return: a tuple of list of strings to be added to the input file, for the `explicit_kpath`
and `explicit_kpath_labels` blocks.
"""
if "mesh" in bands_kpoints.base.attributes.all:
raise ValueError(
"Input should be a list of kpoints along the kpath, but "
f"KpointsData<{bands_kpoints.pk}> contains a mesh"
)
if bands_kpoints.labels is None:
raise ValueError(
f"Input KpointsData<{bands_kpoints.pk}> should contain `labels`"
)
kpoints = bands_kpoints.get_kpoints()
labels = bands_kpoints.labels
# In Wannier90 (from the user guide): Values are in
# fractional coordinates with respect to the primitive
# reciprocal lattice vectors.
explicit_kpath = []
for kpt in kpoints:
explicit_kpath.append(f"{kpt[0]:18.10f} {kpt[1]:18.10f} {kpt[2]:18.10f}")
explicit_kpath_labels = []
for idx, lab in labels:
kpt = kpoints[idx]
path_line = f"{lab} {kpt[0]:18.10f} {kpt[1]:18.10f} {kpt[2]:18.10f}"
explicit_kpath_labels.append(path_line)
return explicit_kpath, explicit_kpath_labels
def _format_block_inputs(block_inputs):
res = []
for name, lines in sorted(block_inputs.items()):
res.append("")
res.append(f"begin {name}")
res.extend(lines)
res.append(f"end {name}")
return res