Structure

Structure(cell::Mat3, atoms::Vector{Atom})

The structure on which the Calculations will be performed.

Structure(cif_file::String)

Creates a Structure from the supplied cif file.

getindex(structure::Structure, i::Int)
getindex(structure::Structure, name::Symbol)
getindex(structure::Structure, el::Element)

Returns the ith atom in structure, or all atoms with name or are of element el.

update_geometry!(str1::Structure, str2::Structure)

Updates the spatial parameters of the atoms and cell of the first structure to those found in the second.

polyhedron(at::Atom, atoms::Vector{Atom}, order::Int)
polyhedron(at::Atom, str::Structure, order::Int)

Returns a polyhedron around the atom, i.e. the order closest atoms. The returned atoms will be ordered according to their distance to the first one. In the case of a structure rather than a set of atoms, the search will be performed over all atoms in the structure.

high_symmetry_kpath(s::Structure, npoints_per_segment::Int; package=QE, kwargs...)

Generates a QE bands calculation compliant high symmetry kpath, to be used with e.g. set_kpoints!(bands_calculation, kpoints).

high_symmetry_kpoints(s::Structure; tolerance = 1e-5)

Returns (kpoints, path) where kpoints are the high-symmetry k-points, and path are the sections of the high symmetry path through the first Brillouin Zone.

international(s::Structure; tolerance=1.0e-5)

Returns the international symbol of the space group of the structure.

niggli_reduce(s::Structure; tolerance=1.0e-5)

Returns the niggli reduced Structure.

symmetry_operators(s::Structure; maxsize=52, tolerance=1.0e-5)

Finds and returns all the rotations and translations that are symmetry operators of the structure.

a(str::Structure)

First lattice vector.

b(str::Structure)

Second lattice vector.

c(str::Structure)

Third lattice vector.

cell_parameters(cell::Mat3)
cell_parameters(str::Structure)

Parameters (a, b, c, α, β, γ)of the calculation cell returned in a NamedTuple.

volume(cell::Mat3)
volume(str::Structure)

Calculates the volume for the unit cell.

create_supercell(structure::Structure, na::Int, nb::Int, nc::Int; make_afm=false)
create_supercell(structure::Structure, na::UnitRange, nb::UnitRange, nc::UnitRange; make_afm=false)

Takes a structure and creates a supercell from it with: the given amount of additional cells if (na::Int, nb::Int, nc::Int) along the a, b, c direction, or amount of cells specified by the ranges i.e. -1:1, -1:1, -1:1 would create a 3x3x3 supercell. If make_afm is set to true all the labels and magnetizations of the magnetic atoms will be reversed in a checkerboard fashion.

scale_cell!(structure::Structure, scalemat::Matrix)

Rescales the cell of the structure.

Atom(name::Symbol, element::Element, position_cart::Point3{Length}, position_cryst::Point3;
     pseudo::String = "",
     projections::Vector{Projection} = Projection[],
     magnetization::Vec3 = Vec3(0.0, 0.0, 0.0),
     dftu::DFTU = DFTU())

Representation of an atom.

The name of the atom is used as an identifier for the atom type, in the sense that atoms with the same pseudo, projections, magnetization and dftu attributes should belong to the same type. This also means that during sanity checks atoms that are not of the same type will be given different names. This is done in this way because it often makes sense to change these parameters on all atoms of the same kind at the same time, but still allow the flexibility to change them for individual atoms as well.

position_cart should have a valid Unitful.Length type such as Ang.

See documentation for Element for further information on this attribute.

set_position!(at::Atom, pos::AbstractVector{T}, unit_cell::Mat3) where {T<:Real}

Updates the position of the atom to this. The unit cell is used to make sure both position_cryst and position_cart are correct.

Element(symbol::Symbol, Z::Int, name::String, atomic_weight::Float64, color::NTuple{3, Float64})

Represents an element. Most conveniently used trough the function element.

element(sym::Symbol)

Returns the predefined Element with symbol sym, i.e. element(:Si) will return the pregenerated Silicon Element.

set_pseudos!(job::Job, set::String; server=job.server, specifier::String="", kwargs...)
set_pseudos!(structure::Structure, set::String; server="localhost", specifier::String="", kwargs...)

Sets the pseudopotentials of the atoms inside the structure (or job.structure) to the ones of set. specifier can be specified as a fuzzy match to select a specific pseudos if multiple pseudopotentials exist in the set. Example:

set_pseudos!(job, "pbesol", specifier="rrkjus")

will select the pseudo file that contains "rrkjus" in the filename.

The pseudos will be searched for in the server.

Projection(orbital::Orbital, start::Int, last::Int)

A Wannier90 Projection, representing an Orbital with indices from start to last.

Orbital(name::String, size::Int, l::Int, mr::Int)

Wannier90 orbital as defined in the Wannier90 User Guide. The name will be written in the projections block of the Wannier90 input.

DFTU(;l ::Int = -1,
      U ::T   = zero(T),
      J0::T  = zero(T),
      α ::T   = zero(T),
      β ::T   = zero(T),
      J ::Vector{T} = T[zero(T)])

DFT+U parameters for a given Atom.