# RAD-tools - Sandbox (mainly condense matter plotting).
# Copyright (C) 2022-2024 Andrey Rybakov
#
# e-mail: anry@uv.es, web: rad-tools.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/>.
r"""
Input-output for |Vampire|_.
"""
__all__ = ["dump_vampire", "dump_mat", "dump_ucf"]
import numpy as np
from radtools.decorate.array import print_2d_array
from radtools.decorate.stats import logo
from radtools.spinham.parameter import ExchangeParameter
meV_TO_J = 1.602176634e-22
[docs]
def dump_vampire(
spinham,
seedname="vampire",
anisotropic=True,
dmi=True,
custom_mask=None,
decimals=5,
materials=None,
nologo=False,
):
"""
Save the Hamiltonian in a Human-readable format.
Parameters
----------
spinham : :py:class:`.SpinHamiltonian`
Spin Hamiltonian to be saved.
seedname : str, default "vampire"
Seedname for the .UCF and .mat files. Extensions are added automatically.
Input file always have the name "input".
anisotropic : bool, default True
Whether to output anisotropic exchange.
dmi : bool, default True
Whether to output DMI exchange.
custom_mask : func, optional
Custom mask for the exchange parameter. Function which take (3,3) numpy:`ndarray`
as an input and returns (3,3) numpy:`ndarray` as an output. If given, then
``anisotropic`` and ``dmi`` parameters are ignored.
decimals : int, default 4
Number of decimals to be printed (only for the exchange values).
materials : list of int, optional
List of materials for the atoms. Has to have the same length as the number of
magnetic atoms in the ``spinham``. Order is the same as in :py:attr:`.SpinHamiltonian.magnetic_atoms`.
If not given, each atom will be considered as a separate material. Starting from 0.
nologo : bool, default False
Whether to print the logo in the output files.
Returns
-------
content : str
Content of the .UCF file if ``filename`` is not given.
"""
dump_ucf(
spinham,
filename=seedname + ".UCF",
anisotropic=anisotropic,
dmi=dmi,
custom_mask=custom_mask,
decimals=decimals,
materials=materials,
nologo=nologo,
)
dump_mat(
spinham,
filename=seedname + ".mat",
materials=materials,
nologo=nologo,
)
with open("input", "w", encoding="utf-8") as file:
file.write(
"#------------------------------------------\n"
f"material:file={seedname}.mat\n"
f"material:unit-cell-file = {seedname}.UCF\n"
"#------------------------------------------\n"
)
def dump_mat(spinham, filename=None, materials=None, nologo=False):
"""
Write .mat file for |Vampire|_.
Parameters
----------
spinham : :py:class:`.SpinHamiltonian`
Spin Hamiltonian to be saved.
filename : str, optional
Name for the .mat file. No extensions is added automatically.
If not given, the output is returned as a string.
materials : list of int, optional
List of materials for the atoms. Has to have the same length as the number of
magnetic atoms in the ``spinham``. Order is the same as in :py:attr:`.SpinHamiltonian.magnetic_atoms`.
If not given, each atom will be considered as a separate material. Starting from 0.
nologo : bool, default False
Whether to print the logo in the output files.
"""
if nologo:
result = []
else:
result = [logo(comment=True, date_time=True) + "\n"]
if materials is not None:
result.append(f"material:num-materials = {max(materials)+1}\n")
else:
result.append(f"material:num-materials = {len(spinham.magnetic_atoms)}\n")
for i, atom in enumerate(spinham.magnetic_atoms):
if materials is None or materials[i] not in materials[:i]:
if materials is not None:
m_i = materials[i] + 1
else:
m_i = i + 1
result.append("#---------------------------------------------------\n")
result.append(f"# Material {m_i} \n")
result.append("#---------------------------------------------------\n")
result.append(f"material[{m_i}]:material-name = {atom.name}\n")
result.append(f"material[{m_i}]:material-element = {atom.type}\n")
result.append(f"material[{m_i}]:atomic-spin-moment={atom.spin}\n")
if atom._spin_direction is not None:
result.append(
f"material[{m_i}]:initial-spin-direction = {atom.spin_direction[0]:.8f},{atom.spin_direction[1]:.8f},{atom.spin_direction[2]:.8f}\n"
)
else:
result.append(f"material[{m_i}]:initial-spin-direction = random\n")
result.append(f"material[{m_i}]:dampling-constant=0.1\n")
result.append(f"material[{m_i}]:uniaxial-anisotropy-constant=0.0\n")
result.append("#---------------------------------------------------\n")
result = "".join(result)
if filename is None:
return "".join(result)
with open(filename, "w", encoding="utf-8") as file:
file.write("".join(result))
def dump_ucf(
spinham,
filename=None,
anisotropic=True,
dmi=True,
custom_mask=None,
decimals=5,
materials=None,
nologo=False,
):
"""
Save the Hamiltonian in a Human-readable format.
Parameters
----------
spinham : :py:class:`.SpinHamiltonian`
Spin Hamiltonian to be saved.
filename : str, optional
Name for the .UCF file. No extension is added automatically.
If not given, the output is returned as a string.
anisotropic : bool, default True
Whether to output anisotropic exchange.
dmi : bool, default True
Whether to output DMI exchange.
custom_mask : func, optional
Custom mask for the exchange parameter. Function which take (3,3) numpy:`ndarray`
as an input and returns (3,3) numpy:`ndarray` as an output. If given, then
``anisotropic`` and ``dmi`` parameters are ignored.
decimals : int, default 4
Number of decimals to be printed (only for the exchange values).
materials : list of int, optional
List of materials for the atoms. Has to have the same length as the number of
magnetic atoms in the ``spinham``. Order is the same as in :py:attr:`.SpinHamiltonian.magnetic_atoms`.
If not given, each atom will be considered as a separate material.
nologo : bool, default False
Whether to print the logo in the output files.
Returns
-------
content : str
Content of the .UCF file if ``filename`` is not given.
"""
original_notation = spinham.notation
spinham.notation = "vampire"
if nologo:
result = []
else:
result = [logo(comment=True, date_time=True) + "\n"]
result.append("# Unit cell size:\n")
result.append(f"{spinham.a:.8f} {spinham.b:.8f} {spinham.c:.8f}\n")
result.append("# Unit cell lattice vectors:\n")
result.append(
print_2d_array(
spinham.a1, borders=False, print_result=False, fmt=".8f"
).lstrip()
+ "\n"
)
result.append(
print_2d_array(
spinham.a2, borders=False, print_result=False, fmt=".8f"
).lstrip()
+ "\n"
)
result.append(
print_2d_array(
spinham.a3, borders=False, print_result=False, fmt=".8f"
).lstrip()
+ "\n"
)
result.append("# Atoms\n")
result.append(f"{len(spinham.magnetic_atoms)} {len(np.unique(materials))}\n")
atom_indices = {}
for a_i, atom in enumerate(spinham.magnetic_atoms):
result.append(
f"{a_i} {atom.position[0]:.8f} {atom.position[1]:.8f} {atom.position[2]:.8f}"
)
if materials is not None:
result.append(f" {materials[a_i]}")
else:
result.append(f" {a_i}")
result.append("\n")
atom_indices[atom] = a_i
result.append("# Interactions\n")
result.append(f"{len(spinham)} tensorial\n")
IID = 0
for atom1, atom2, (i, j, k), J in spinham:
if custom_mask is not None:
J = ExchangeParameter(custom_mask(J))
else:
if not dmi:
J = ExchangeParameter(matrix=J.matrix - J.dmi_matrix)
if not anisotropic:
J = ExchangeParameter(matrix=J.matrix - J.aniso)
J = J * meV_TO_J
fmt = f"{7+decimals}.{decimals}e"
result.append(
f"{IID:<2} {atom_indices[atom1]:>2} {atom_indices[atom2]:>2} {i:>2} {j:>2} {k:>2} "
)
result.append(f"{J.xx:{fmt}} {J.xy:{fmt}} {J.xz:{fmt}} ")
result.append(f"{J.yx:{fmt}} {J.yy:{fmt}} {J.yz:{fmt}} ")
result.append(f"{J.zx:{fmt}} {J.zy:{fmt}} {J.zz:{fmt}}\n")
IID += 1
spinham.notation = original_notation
result = "".join(result)
if filename is None:
return result
with open(filename, "w", encoding="utf-8") as file:
file.write(result)
