Source code for grogupy.physics.magnetic_entity

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import copy
from typing import TYPE_CHECKING, Any, Iterator, Union

from numpy.typing import NDArray

if TYPE_CHECKING:
    from grogupy.physics import Hamiltonian

import numpy as np
import sisl

from grogupy import __version__
from grogupy._core.utilities import arrays_lists_equal, arrays_None_equal

from .utilities import (
    blow_up_orbindx,
    calculate_anisotropy_tensor,
    fit_anisotropy_tensor,
    interaction_energy,
    parse_magnetic_entity,
    second_order_energy,
)


[docs] class MagneticEntity: """This class contains the data and the methods related to the magnetic entities. It sets up the instance based on the indexing of the Hamiltonian by the ``atom``, ``l`` and orbital (``orb``) parameters. There are four possible input types: 1. Cluster: a list of atoms 2. AtomShell: one atom and a list of shells indexed in the atom or a list of atoms and a list of lists containing the shells 3. AtomOrbital: one atom and a list of orbitals indexed in the atom or a list of atoms and a list of lists containing the orbitals 4. Orbitals: a list of orbitals indexed in the Hamiltonian Parameters ---------- infile: Union[str, tuple[Union[sisl.physics.Hamiltonian, Hamiltonian], Union[sisl.physics.DensityMatrix, None]]] Either the path to the .fdf file or a tuple of sisl or grogupy hamiltonian and a sisl density matrix atom: Union[None, int, list[int]], optional Defining atom (or atoms) in the unit cell forming the magnetic entity, by default None l: Union[None, int, list[int], list[list[int]]], optional Defining the angular momentum channel, by default None orb: Union[None, int, list[int], list[list[int]]], optional Defining the orbital index in the Hamiltonian or on the atom, by default None Examples -------- Creating a magnetic entity can be done by giving the Hamiltonian from the DFT calculation and somehow specifying the corresponding atoms and orbitals. The following examples show you how to create magnetic entities in the **Fe3GeTe2** system. You can compare the tags of the ``MagneticEntity`` to the input parameters, to understand how to build the magnetic entity, that suits your needs. >>> fdf_path = "/Users/danielpozsar/Downloads/Fe3GeTe2/Fe3GeTe2.fdf" To define a Cluster of atoms use a dictionary that only contains atoms. >>> magnetic_entity = MagneticEntity(fdf_path, atom=[3,4,5]) >>> print(magnetic_entity.tag) 3Fe(l:All)--4Fe(l:All)--5Fe(l:All) To define a magnetic entity with a single atom, but with specific shells use both the ``atom`` and ``l`` key in the dictionary. >>> magnetic_entity = MagneticEntity(fdf_path, atom=5, l=[[1,2,3]]) >>> print(magnetic_entity.tag) 5Fe(l:1-2-3) Or you can define multiple atoms with different shells: >>> magnetic_entity = MagneticEntity(fdf_path, atom=[4,5], l=[[1],[1,2,3]]) >>> print(magnetic_entity.tag) 4Fe(l:1)--5Fe(l:1-2-3) To define a magnetic entity with a single atom, but with specific orbitals use both the ``atom`` and ``orb`` key in the dictionary. Be aware that these orbitals are indexed inside the atom, not in the total Hamiltonian. >>> magnetic_entity = MagneticEntity(fdf_path, atom=5, orb=[[1,2,3,4,5,6,7,8,9,10]]) >>> print(magnetic_entity.tag) 5Fe(o:1-2-3-4-5-6-7-8-9-10) Or you can define multiple atoms with different orbitals: >>> magnetic_entity = MagneticEntity(fdf_path, atom=[4,5], orb=[[1],[1,2,3,4,5,6,7,8,9,10]]) >>> print(magnetic_entity.tag) 4Fe(o:1)--5Fe(o:1-2-3-4-5-6-7-8-9-10) And finally you can use only the ``orb`` key to directly index the orbitals from the Hamiltonian. >>> magnetic_entity = MagneticEntity(fdf_path, orb=[1,10,30,40,50]) >>> print(magnetic_entity.tag) 0Te(o:1-10)--2Ge(o:4)--3Fe(o:1-11) Methods ------- calculate_energies(weights) : Calculates the energies of the infinitesimal rotations. calculate_anisotropy() : Calculates the anisotropy matrix and the consistency from the energies. copy() : Return a copy of this MagneticEntity Attributes ---------- _orbital_box_indices : NDArray The ORBITAL BOX indices _atom : NDArray The list of atoms in the magnetic entity _l : list[list[Union[None, int]]] The list of l in the magnetic entity, None if it is incomplete _spin_box_indices : NDArray The SPIN BOX indices _total_mulliken: Union[None, NDArray] Sisl Mulliken charges from the total atom _local_mulliken: Union[None, NDArray] Sisl Mulliken charges from the given orbitals SBS : int Length of the SPIN BOX indices _xyz : NDArray The coordinates of the magnetic entity (it can consist of many atoms) _xyz_center : NDArray The center of coordinates for the magnetic entity _tag : str The description of the magnetic entity _Vu1 : list[list[float]] The list of the first order rotations _Vu2 : list[list[float]] The list of the second order rotations _Gii : list[NDArray] The list of the projected Greens functions energies : Union[None, NDArray] The calculated energies for each direction K : Union[None, NDArray] The magnetic anisotropy, by default None K_consistency : Union[None, float] Consistency check on the diagonal K elements, by default None """ number_of_entities: int = 0
[docs] def __init__( self, infile: Union[ str, tuple[ sisl.physics.Hamiltonian, Union[sisl.physics.DensityMatrix, None], ], ], atom: Union[None, int, list[int]] = None, l: Union[None, int, list[int], list[list[int]]] = None, orb: Union[None, int, list[int], list[list[int]]] = None, ) -> None: """Initialize the magnetic entity.""" if isinstance(infile, str): # get sisl sile sile = sisl.get_sile(infile) # load density and hamiltonian self._dh: sisl.physics.Hamiltonian = sile.read_hamiltonian() try: self._ds: Union[None, sisl.physics.DensityMatrix] = ( sile.read_density_matrix() ) except: self._ds: Union[None, sisl.physics.DensityMatrix] = None self.infile: str = infile elif isinstance(infile, tuple): self._dh: sisl.physics.Hamiltonian = infile[0] self._ds: Union[None, sisl.physics.DensityMatrix] = infile[1] self.infile: str = "Unknown!" else: raise Exception("Cannot setup without path or sisl objects!") atom, l, orbital, tag = parse_magnetic_entity(self._dh, atom, l, orb) self._atom: NDArray = np.array([atom]).flatten() self._l = l self._orbital_box_indices: NDArray = np.array(orbital).flatten() self._tags = tag # try to get Mulliken charges if self._ds is not None: self._total_mulliken: Union[None, NDArray] = self._ds.mulliken()[ :, self._dh.a2o(self._atom, all=True) ] self._local_mulliken: Union[None, NDArray] = self._ds.mulliken()[ :, self._orbital_box_indices ] # this is the spin moment instwad of the magnetic moment self._total_mulliken[:, 1:] = self._total_mulliken[:, 1:] / 2 self._local_mulliken[:, 1:] = self._local_mulliken[:, 1:] / 2 else: self._total_mulliken: Union[None, NDArray] = None self._local_mulliken: Union[None, NDArray] = None self._xyz: NDArray = np.array([self._dh.xyz[i] for i in self._atom]) # initialize simulation parameters self._Vu1: list[list[NDArray]] = [] self._Vu2: list[list[NDArray]] = [] self._Gii: Union[list[list[NDArray]], list[NDArray]] = [] self.energies: Union[None, NDArray] = None self._K: Union[None, NDArray] = None self._K_consistency: Union[None, float] = None MagneticEntity.number_of_entities += 1
def __getstate__(self): return self.__dict__.copy() def __setstate__(self, state): self.__dict__ = state def __add__(self, value): if not isinstance(value, MagneticEntity): raise Exception("Only MagneticEntity instances can be added!") # do not change the current instance new = self.copy() # reset the values that does not make sense for a new magnetic entity new.reset() # update out instance # accept both kinds of hamiltonian if not arrays_lists_equal(new._dh.Hk().toarray(), value._dh.Hk().toarray()): raise Exception("The sisl Hamiltonians are not the same!") if not arrays_lists_equal(new._dh.Sk().toarray(), value._dh.Sk().toarray()): raise Exception("The sisl Overlap matrices are not the same!") new._atom = np.hstack((new._atom, value._atom)) new._l = new._l + value._l new._orbital_box_indices = np.hstack( (new._orbital_box_indices, value._orbital_box_indices) ) new._tags = new._tags + value._tags new._xyz = np.vstack((new._xyz, value._xyz)) return new def __eq__(self, value): if isinstance(value, MagneticEntity): # if the IDs are identical, skip comaprison if id(self) == id(value): return True # if there are sisl Hamiltonians, then compare if self._dh is None and value._dh is None: pass else: if not arrays_lists_equal( self._dh.Hk().toarray(), value._dh.Hk().toarray() ): return False if not arrays_lists_equal( self._dh.Sk().toarray(), value._dh.Sk().toarray() ): return False if not arrays_lists_equal( self._ds.Dk().toarray(), value._ds.Dk().toarray() ): return False if not arrays_lists_equal( self._ds.Sk().toarray(), value._ds.Sk().toarray() ): return False if not self.infile == value.infile: return False if not arrays_lists_equal(self._atom, value._atom): return False if not self._l == value._l: return False if not arrays_lists_equal( self._orbital_box_indices, value._orbital_box_indices ): return False if not self._tags == value._tags: return False if not arrays_lists_equal(self._total_mulliken, value._total_mulliken): return False if not arrays_lists_equal(self._local_mulliken, value._local_mulliken): return False if not arrays_lists_equal(self._xyz, value._xyz): return False if not arrays_lists_equal(self._Vu1, value._Vu1): return False if not arrays_lists_equal(self._Vu2, value._Vu2): return False if not arrays_lists_equal(self._Gii, value._Gii): return False if not arrays_None_equal(self.energies, value.energies): return False if not arrays_None_equal(self._K, value._K): return False # Checking K_consistency separately # if both are None, then pass and no other check is perfomred because of elif if self._K_consistency is None and value.K_consistency is None: pass # if either one is None, but the other is not, then return false elif self._K_consistency is not None and value.K_consistency is None: return False elif self._K_consistency is None and value.K_consistency is not None: return False # If neither of them is None, compare them elif not np.isclose(self._K_consistency, value._K_consistency): return False return True else: return False def __repr__(self) -> str: """String representation of the instance.""" out = f"<grogupy.MagneticEntity tag={self.tag}, SBS={self.SBS}>" return out @property def tag(self): """The description of the magnetic entity""" return "--".join(self._tags) @property def _spin_box_indices(self) -> NDArray: """The spin box indices of the magnetic entity""" return blow_up_orbindx(self._orbital_box_indices) @property def SBS(self) -> int: """The spin box size of the magnetic entity""" return len(self._spin_box_indices) @property def SBI(self) -> NDArray: """The spin box indices of the magnetic entity""" return self._spin_box_indices @property def xyz_center(self) -> NDArray: """The mean of the position of the atoms that are in the magnetic entity.""" return self._xyz.mean(axis=0) @property def total_Q(self) -> Union[NDArray, None]: """The total charge of the atom or the atoms of magnetic entity.""" # check if DM is available if self._total_mulliken is None: return None return self._total_mulliken[0].sum() @property def total_S(self) -> Union[None, float]: """Spin moment of the atom or the atoms of the magnetic entity.""" # check if DM is available if self._total_mulliken is None: return None if self._total_mulliken.shape[0] == 2: return self._total_mulliken[1].sum() elif self._total_mulliken.shape[0] in {3, 4}: return np.linalg.norm(self._total_mulliken.sum(axis=1)[1:]).astype(float) else: Exception("Unpolarized DFT calculation cannot be used!") @property def total_Sx(self) -> Union[None, float]: """Sx of the atom or the atoms of the magnetic entity.""" # check if DM is available if self._total_mulliken is None: return None if self._total_mulliken.shape[0] == 2: return 0 elif self._total_mulliken.shape[0] in {3, 4}: return self._total_mulliken[1].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def total_Sy(self) -> Union[None, float]: """Sy of the atom or the atoms of the magnetic entity.""" # check if DM is available if self._total_mulliken is None: return None if self._total_mulliken.shape[0] == 2: return 0 elif self._total_mulliken.shape[0] in {3, 4}: return self._total_mulliken[2].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def total_Sz(self) -> Union[None, float]: """Sz of the atom or the atoms of the magnetic entity.""" # check if DM is available if self._total_mulliken is None: return None if self._total_mulliken.shape[0] == 2: return self._total_mulliken[1].sum() elif self._total_mulliken.shape[0] in {3, 4}: return self._total_mulliken[3].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def local_Q(self) -> Union[None, float]: """The charge of the magnetic entity.""" # check if DM is available if self._local_mulliken is None: return None return self._local_mulliken[0].sum() @property def local_S(self) -> Union[None, float]: """Spin moment of the atom or the atoms of the magnetic entity.""" # check if DM is available if self._local_mulliken is None: return None if self._local_mulliken.shape[0] == 2: return self._local_mulliken[1].sum() elif self._local_mulliken.shape[0] in {3, 4}: return np.linalg.norm(self._local_mulliken.sum(axis=1)[1:]).astype(float) else: Exception("Unpolarized DFT calculation cannot be used!") @property def local_Sx(self) -> Union[None, float]: """Sx of the magnetic entity.""" # check if DM is available if self._local_mulliken is None: return None if self._local_mulliken.shape[0] == 2: return 0 elif self._local_mulliken.shape[0] in {3, 4}: return self._local_mulliken[1].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def local_Sy(self) -> Union[None, float]: """Sy of the magnetic entity.""" # check if DM is available if self._local_mulliken is None: return None if self._local_mulliken.shape[0] == 2: return 0 elif self._local_mulliken.shape[0] in {3, 4}: return self._local_mulliken[2].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def local_Sz(self) -> Union[None, float]: """Sz of the magnetic entity.""" # check if DM is available if self._local_mulliken is None: return None if self._local_mulliken.shape[0] == 2: return self._local_mulliken[1].sum() elif self._local_mulliken.shape[0] in {3, 4}: return self._local_mulliken[3].sum() else: Exception("Unpolarized DFT calculation cannot be used!") @property def energies_meV(self) -> Union[None, float]: """The energies, but in meV.""" if self.energies is None: return None else: return self.energies * sisl.unit_convert("eV", "meV") @property def energies_mRy(self) -> Union[None, NDArray]: """The energies, but in mRy.""" if self.energies is None: return None else: return self.energies * sisl.unit_convert("eV", "mRy") @property def energies_J(self) -> Union[None, NDArray]: """The energies, but in J.""" if self.energies is None: return None else: return self.energies * sisl.unit_convert("eV", "J") @property def K(self) -> Union[None, NDArray]: """The anisotropy tensor, in meV.""" return self._K @property def K_meV(self) -> Union[None, NDArray]: """The anisotropy tensor, but in meV.""" if self.K is None: return None else: return self.K * sisl.unit_convert("eV", "meV") @property def K_mRy(self) -> Union[None, NDArray]: """The anisotropy tensor, but in mRy.""" if self.K is None: return None else: return self.K * sisl.unit_convert("eV", "mRy") @property def K_J(self) -> Union[None, NDArray]: """The anisotropy tensor, but in J.""" if self.K is None: return None else: return self.K * sisl.unit_convert("eV", "J") @property def K_consistency(self) -> Union[None, NDArray]: """The consistency check, in meV.""" return self._K_consistency @property def K_consistency_meV(self) -> Union[None, NDArray]: """The consistency check, but in meV.""" if self.K_consistency is None: return None else: return self.K_consistency * sisl.unit_convert("eV", "meV") @property def K_consistency_mRy(self) -> Union[None, NDArray]: """The consistency check, but in mRy.""" if self.K_consistency is None: return None else: return self.K_consistency * sisl.unit_convert("eV", "mRy") @property def K_consistency_J(self) -> Union[None, NDArray]: """The consistency check, but in J.""" if self.K_consistency is None: return None else: return self.K_consistency * sisl.unit_convert("eV", "J") def reset(self) -> None: """Resets the simulation results.""" self._Vu1: list[list[NDArray]] = [] self._Vu2: list[list[NDArray]] = [] self._Gii: Union[list[list[NDArray]], list[NDArray]] = [] self.energies: Union[None, NDArray] = None self._K: Union[None, NDArray] = None self._K_consistency: Union[None, float] = None def calculate_energies( self, weights: NDArray, append: bool = False, third_direction: bool = False ) -> None: """Calculates the energies of the infinitesimal rotations. It uses the instance properties to calculate the energies and dumps the results to the ``energies`` property. Parameters ---------- weights : NDArray The weights of the energy contour integral append: bool, optional If it is True, then the energy of a single rotation is appended to the energies from the temporary storages, by default False third_direction : bool, optional Wether to use a linear combination of the two perpendicular orientation, by default False """ if append: storage: list[float] = [] Gii = self._Gii_tmp # iterate over the first and second order local perturbations V1 = self._Vu1_tmp V2 = self._Vu2_tmp # fill up the magnetic entities dictionary with the energies storage.append(second_order_energy(V1[0], V2[0], Gii, weights)) storage.append(interaction_energy(V1[0], V1[1], Gii, Gii, weights)) storage.append(interaction_energy(V1[1], V1[0], Gii, Gii, weights)) storage.append(second_order_energy(V1[1], V2[1], Gii, weights)) if third_direction: storage.append(second_order_energy(V1[2], V2[2], Gii, weights)) if self.energies is None: self.energies = np.array(storage) else: self.energies = np.vstack((self.energies, np.array(storage))) else: energies: list[list[float]] = [] for i, Gii in enumerate(self._Gii): storage: list[float] = [] # iterate over the first and second order local perturbations V1 = self._Vu1[i] V2 = self._Vu2[i] # fill up the magnetic entities dictionary with the energies storage.append(second_order_energy(V1[0], V2[0], Gii, weights)) storage.append(interaction_energy(V1[0], V1[1], Gii, Gii, weights)) storage.append(interaction_energy(V1[1], V1[0], Gii, Gii, weights)) storage.append(second_order_energy(V1[1], V2[1], Gii, weights)) if third_direction: storage.append(second_order_energy(V1[2], V2[2], Gii, weights)) energies.append(storage) self.energies: Union[None, NDArray] = np.array(energies) def calculate_anisotropy(self) -> None: """Calculates the anisotropy matrix and the consistency from the energies. It uses the instance properties to calculate the anisotropy matrix and the consistency and dumps them to the `K`, `K_consistency` properties. """ if self.energies is None: raise Exception("Energies missing for anisotropy!") K, K_consistency = calculate_anisotropy_tensor(self.energies) self._K: Union[None, NDArray] = K self._K_consistency: Union[None, float] = K_consistency def fit_anisotropy_tensor(self, ref_xcf: list[dict]) -> None: """Fits the anisotropy tensor to the energies. It uses a fitting method to calculate the anisotropy tensor from the reference directions and its different representations and dumps them to the ``K`` property. It writes ``None`` to the ``K_consistency`` property. Parameters ---------- ref_xcf: list[dict] The reference directions containing the orientation and perpendicular directions """ if self.energies is None: raise Exception("Energies missing for anisotropy!") K = fit_anisotropy_tensor(self.energies, ref_xcf) self._K: Union[None, NDArray] = K # it is not relevant with this method self._K_consistency: Union[float, None] = None def copy(self): """Returns the deepcopy of the instance. Returns ------- MagneticEntity The copied instance. """ return copy.deepcopy(self)
[docs] class MagneticEntityList: """List of MagneticEntities. It supports easier attribute access across the MagneticEntities in the list. """
[docs] def __init__( self, magnetic_entities: Union[None, list[MagneticEntity], NDArray] = None ): if magnetic_entities is None: self.__magnetic_entities = [] elif isinstance(magnetic_entities, MagneticEntityList): self.__magnetic_entities = magnetic_entities.__magnetic_entities elif isinstance(magnetic_entities, list) or isinstance( magnetic_entities, np.ndarray ): self.__magnetic_entities = list(magnetic_entities) else: raise Exception(f"Bad input type: {type(magnetic_entities)}!")
def __len__(self): return len(self.__magnetic_entities) def __iter__(self) -> Iterator[MagneticEntity]: return iter(self.__magnetic_entities) def __add__(self, other): if isinstance(other, MagneticEntityList): other = other.__magnetic_entities elif isinstance(other, list): pass elif isinstance(other, np.ndarray): other = other.tolist() else: raise Exception( "Only list, np.ndparray and MagneticEntityList can be added to MagneticEntityList" ) return MagneticEntityList(self.__magnetic_entities + other) def __getstate__(self): state = self.__dict__.copy() out = [] for m in state["_MagneticEntityList__magnetic_entities"]: out.append(m.__getstate__()) state["_MagneticEntityList__magnetic_entities"] = out return state def __setstate__(self, state): out = [] for m in state["_MagneticEntityList__magnetic_entities"]: temp = object.__new__(MagneticEntity) temp.__setstate__(m) out.append(temp) state["_MagneticEntityList__magnetic_entities"] = out self.__dict__ = state def __getattr__(self, name) -> NDArray: try: return np.array( [m.__getattribute__(name) for m in self.__magnetic_entities] ) except: return np.array( [m.__getattribute__(name) for m in self.__magnetic_entities], dtype=object, ) def __getitem__(self, item: int) -> MagneticEntity: return self.__magnetic_entities[item] def __repr__(self) -> str: """String representation of the instance.""" out = f"<grogupy.MagneticEntityList length={len(self.__magnetic_entities)}>" return out def __str__(self) -> str: """String of the instance.""" out = "[" + "\n".join([p.__repr__() for p in self.__magnetic_entities]) + "]" return out def append(self, item): """Appends to the magnetic entity list.""" if isinstance(item, MagneticEntity): self.__magnetic_entities.append(item) else: raise Exception("This class is reserved for MagneticEntity instances only!") def tolist(self) -> list[MagneticEntity]: """Returns a list from the underlying data. Returns ------- list The magnetic entities in a list format. """ return self.__magnetic_entities def toarray(self) -> NDArray: """Returns a numpy array from the underlying data. Returns ------- NDArray The magnetic entities in a numpy array. """ return np.array(self.__magnetic_entities, dtype=object)
if __name__ == "__main__": pass