# ================================== LICENSE ===================================
# Magnopy - Python package for magnons.
#
# Copyright (C) 2023 Magnopy Team
#
# e-mail: anry@uv.es, web: magnopy.org
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <https://www.gnu.org/licenses/>.
# ================================ END LICENSE =================================
import numpy as np
from wulfric.crystal import get_distance
from magnopy._parameters._p22 import from_dmi, from_iso
from magnopy._spinham._convention import Convention
from magnopy._spinham._hamiltonian import SpinHamiltonian
# Save local scope at this moment
old_dir = set(dir())
old_dir.add("old_dir")
[docs]
def load_tb2j(
filename,
spin_values=None,
spglib_types=None,
g_factors=None,
missing_bonds="restore",
when_present="raise error",
quiet=True,
) -> SpinHamiltonian:
r"""
Reads spin Hamiltonian from the "exchange.out" file produced by |TB2J|_.
Parameters
----------
filename : str
Path to the "exchange.out" file produced by |TB2J|_.
spin_values : (M, ) iterable of floats, optional
Spin values for all magnetic atoms. Order is the same as in |TB2J|_ file. Magnetic
atoms are defined as those that have at least one parameter associated with them.
If none given, Magnopy sets spin value as :math:`|\boldsymbol{m} / g_{factor}|`
for each spin, where :math:`\boldsymbol{m}` is the magnetic moment, read from the
|TB2J|_ file.
spglib_types : (M_prime, ) iterable of ints, optional
Spglib types for all atoms (not only for magnetic ones, but for all). Order is the
same as in |TB2J|_ file. If none given, then there will be no "spglib_types" key
in ``spinham.atoms``.
g_factors : (M, ) iterable of floats, optional
g-factors for all atoms. Order is the same as in |TB2J|_ file. If none given, then
Magnopy sets :math:`g = 2` for all atoms.
missing_bonds : bool, default "restore"
.. versionadded:: 0.5.2
What to do if some of the equivalent bonds are missing (see
:ref:`user-guide_theory-behind_equivalent-parameters`
and :ref:`user-guide_theory-behind_convention_multiple-counting` for more details
on equivalent bonds). Case-insensitive. Supported options are
* "restore" (default)
Magnopy adds missing equivalent bonds, by inserting additional parameters.
* "ignore"
Magnopy does nothing.
when_present : str, default "raise error"
.. versionadded:: 0.5.2
What to do if the exact same interaction is repeated twice in the file.
See :py:meth:`.SpinHamiltonian.add` for supported values.
quiet : bool, default True
If ``False``, warnings are printed when distances between atoms computed by
Magnopy are different from the distances read from the |TB2J|_ file. This is a
legacy feature, kept for the sake of backward compatibility. See Notes for
details.
Returns
-------
spinham : :py:class:`.SpinHamiltonian`
Spin Hamiltonian, that is built from the |TB2J|_ file.
Raises
------
ValueError
If ``spin_values`` is provided and its length does not match the number of
magnetic atoms in the Hamiltonian.
ValueError
If ``spglib_types`` is provided and its length does not match the number of
atoms in the Hamiltonian.
Notes
-----
|TB2J|_ outputs distances between atoms for each exchange bond. Magnopy do not use
those, but rather computes distances based on the unit cell and atom positions if
necessary. At the moment of reading the file it can check if the distance read from
the file is different from the computed one and print a warning if ``quiet=False``.
Computed and read distances tend to differ in the last digits, since the unit cell is
provided with the same precision as the distance in the |TB2J|_ file.
"""
minor_sep = "-" * 88
garbage = str.maketrans(
{"(": None, ")": None, "[": None, "]": None, ",": None, "'": None}
)
# Do not correct spelling, it is taken from TB2J.
cell_flag = "Cell (Angstrom):"
atoms_flag = "Atoms:"
atom_end_flag = "Total"
exchange_flag = "Exchange:"
iso_flag = "J_iso:"
aniso_flag = "J_ani:"
dmi_flag = "DMI:"
file = open(filename, "r", encoding="utf-8")
# model = SpinHamiltonian(convention="TB2J")
line = True
# Read everything before exchange
while line:
line = file.readline()
# Read cell
if line and cell_flag in line:
a1 = file.readline().split()
a2 = file.readline().split()
a3 = file.readline().split()
cell = np.array(
[
list(map(float, a1)),
list(map(float, a2)),
list(map(float, a3)),
]
)
# Read atoms
if line and atoms_flag in line:
atoms = dict(names=[], positions=[], magnetic_moments=[], charges=[])
line = file.readline()
line = file.readline()
line = file.readline().split()
i = 0
while line and atom_end_flag not in line:
try:
# Slicing is not used intentionally.
magmom = tuple(map(float, [line[5], line[6], line[7]]))
except IndexError:
magmom = float(line[5])
try:
charge = float(line[4])
except IndexError:
charge = None
position = np.array(tuple(map(float, line[1:4]))) @ np.linalg.inv(cell)
atoms["names"].append(line[0])
atoms["positions"].append(position)
atoms["magnetic_moments"].append(magmom)
atoms["charges"].append(charge)
line = file.readline().split()
i += 1
# Check if the exchange section is reached
if line and exchange_flag in line:
break
# Populate g_factors of atoms
if g_factors is None:
g_factors = [2.0 for _ in range(len(atoms["names"]))]
atoms["g_factors"] = g_factors
# Create a spin Hamiltonian
spinham = SpinHamiltonian(
cell=cell, atoms=atoms, convention=Convention.get_predefined(name="tb2j")
)
# Prepare index mapping for atom names
index_mapping = {}
# Names of the atoms are unique in the TB2J files
for index, name in enumerate(spinham.atoms.names):
index_mapping[name] = index
# Read exchange (22) parameters
while line:
while line and minor_sep not in line:
line = file.readline()
line = file.readline().translate(garbage).split()
atom1 = index_mapping[line[0]]
atom2 = index_mapping[line[1]]
ijk = tuple(map(int, line[2:5]))
distance = float(line[-1])
iso = None
aniso = None
dmi = None
while line and minor_sep not in line:
line = file.readline()
# Read isotropic exchange
if line and iso_flag in line:
iso = float(line.split()[-1])
# Read anisotropic exchange
if line and aniso_flag in line:
aniso = np.array(
[
list(map(float, file.readline().translate(garbage).split())),
list(map(float, file.readline().translate(garbage).split())),
list(map(float, file.readline().translate(garbage).split())),
]
)
# Read DMI
if line and dmi_flag in line:
dmi = tuple(map(float, line.translate(garbage).split()[-3:]))
parameter = np.zeros((3, 3), dtype=float)
if iso is not None:
parameter = parameter + from_iso(iso=iso)
if dmi is not None:
parameter = parameter + from_dmi(dmi=dmi)
# Remember: aniso might be not traceless in the TB2J files
if aniso is not None:
parameter = parameter + aniso
spinham.add(
nus=[ijk],
alphas=[atom1, atom2],
parameter=parameter,
when_present=when_present,
)
computed_distance = get_distance(spinham.cell, spinham.atoms, atom1, atom2, ijk)
if abs(computed_distance - distance) > 0.001 and not quiet:
print(
"\nComputed distance is a different from the read one:\n"
+ f" Computed: {computed_distance:.4f}\n "
+ f"Read: {distance:.4f}\n"
)
# Populate spin_values of atoms
if spin_values is not None:
if len(spin_values) != spinham.M:
raise ValueError(
f"Expected {spinham.M} spin values, got {len(spin_values)}"
)
true_spin_values = [0.0 for _ in spinham.atoms.names]
for i in range(len(spin_values)):
true_spin_values[spinham.map_to_all[i]] = spin_values[i]
else:
true_spin_values = [
float(np.linalg.norm(atoms["magnetic_moments"][alpha]))
/ atoms["g_factors"][alpha]
for alpha in range(len(atoms["names"]))
]
spinham.atoms["spins"] = true_spin_values
# Populate spglib_types of atoms
if spglib_types is not None:
if len(spglib_types) != len(spinham.atoms.names):
raise ValueError(
f"Expected {len(spinham.atoms.names)} spglib types, got {len(spglib_types)}"
)
spinham.atoms["spglib_types"] = [int(_) for _ in spglib_types]
missing_bonds = missing_bonds.lower()
if missing_bonds == "restore":
spinham.restore_missing_parameters(strategy="mean")
else:
if missing_bonds != "ignore":
raise ValueError(
f"Unsupported value for missing_bonds. Expected 'restore' or 'ignore', got {missing_bonds}."
)
spinham._reset_internals()
return spinham
# Populate __all__ with objects defined in this file
__all__ = list(set(dir()) - old_dir)
# Remove all semi-private objects
__all__ = [i for i in __all__ if not i.startswith("_")]
del old_dir
