grogupy.physics.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_indicesNDArray: The ORBITAL BOX indices
_total_orbital_box_indicesNDArray: The ORBITAL BOX indices for the whole atom
_atomNDArray: The list of atoms in the magnetic entity
_llist[list[Union[None, int]]]: The list of l in the magnetic entity, None if it is incomplete
_spin_box_indicesNDArray: 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
SBSint: Length of the SPIN BOX indices
_xyzNDArray: The coordinates of the magnetic entity (it can consist of many atoms)
_xyz_centerNDArray: The center of coordinates for the magnetic entity
_tagstr: The description of the magnetic entity
_Vu1list[list[float]]: The list of the first order rotations
_Vu2list[list[float]]: The list of the second order rotations
_Giilist[NDArray]: The list of the projected Greens functions
energiesUnion[None, NDArray]: The calculated energies for each direction
KUnion[None, NDArray]: The magnetic anisotropy, by default None
K_consistencyUnion[None, float]: Consistency check on the diagonal K elements, by default None
dh_ds_id: str: Hash of the underlying system so MagneticEntities cannot be mixed between Hamiltonians
cell: NDArray: Cell size of the underlying system so MagneticEntities cannot be mixed between Hamiltonians

__init__(infile: str | tuple[Hamiltonian, DensityMatrix | None], atom: None | int | list[int] = None, l: None | int | list[int] | list[list[int]] = None, orb: None | int | list[int] | list[list[int]] = None) → None[source]: Initialize the magnetic entity.

Methods

`__init__`(infile[, atom, l, orb])	Initialize the magnetic entity.
`calculate_anisotropy`()	Calculates the anisotropy matrix and the consistency from the energies.
`calculate_energies`(weights[, append, ...])	Calculates the energies of the infinitesimal rotations.
`copy`()	Returns the deepcopy of the instance.
`fit_anisotropy_tensor`(ref_xcf)	Fits the anisotropy tensor to the energies.
`reset`()	Resets the simulation results.

Attributes

`K`	The anisotropy tensor, in meV.
`K_J`	The anisotropy tensor, but in J.
`K_consistency`	The consistency check, in meV.
`K_consistency_J`	The consistency check, but in J.
`K_consistency_mRy`	The consistency check, but in mRy.
`K_consistency_meV`	The consistency check, but in meV.
`K_mRy`	The anisotropy tensor, but in mRy.
`K_meV`	The anisotropy tensor, but in meV.
`SBI`	The spin box indices of the magnetic entity
`SBS`	The spin box size of the magnetic entity
`cell`	The cell of the Hamiltonian.
`dh_ds_id`	The ID of the Hamiltonian and the Density Matrix.
`energies_J`	The energies, but in J.
`energies_mRy`	The energies, but in mRy.
`energies_meV`	The energies, but in meV.
`local_Q`	The charge of the magnetic entity.
`local_S`	Spin moment of the magnetic entity.
`local_Sx`	Sx of the magnetic entity.
`local_Sy`	Sy of the magnetic entity.
`local_Sz`	Sz of the magnetic entity.
`number_of_entities`
`tag`	The description of the magnetic entity
`total_Q`	The total charge of the atom or the atoms of the magnetic entity.
`total_S`	Total spin moment of the atom or the atoms of the magnetic entity.
`total_Sx`	Total Sx of the atom or the atoms of the magnetic entity.
`total_Sy`	Total Sy of the atom or the atoms of the magnetic entity.
`total_Sz`	Total Sz of the atom or the atoms of the magnetic entity.
`xyz_center`	The mean of the position of the atoms that are in the magnetic entity.