API reference
This page provides a plain list of all documented functions, structs, modules and macros in DFTK. Note that this list is neither structured, complete nor particularly clean, so it only provides rough orientation at the moment. The best reference is the code itself.
DFTK.timer — ConstantTimerOutput object used to store DFTK timings.
DFTK.AbstractArchitecture — TypeAbstract supertype for architectures supported by DFTK.
DFTK.AdaptiveBands — TypeDynamically adapt number of bands to be converged to ensure that the orbitals of lowest occupation are occupied to at most occupation_threshold. To obtain rapid convergence of the eigensolver a gap between the eigenvalues of the last occupied orbital and the last computed (but not converged) orbital of gap_min is ensured.
DFTK.Applyχ0Model — TypeFull χ0 application, optionally dropping terms or disabling Sternheimer. All keyword arguments passed to apply_χ0.
DFTK.AtomicLocal — TypeAtomic local potential defined by model.atoms.
DFTK.AtomicNonlocal — TypeNonlocal term coming from norm-conserving pseudopotentials in Kleinmann-Bylander form. $\text{Energy} = \sum_a \sum_{ij} \sum_{n} f_n <ψ_n|p_{ai}> D_{ij} <p_{aj}|ψ_n>.$
DFTK.BlowupAbinit — TypeBlow-up function as used in Abinit.
DFTK.BlowupCHV — TypeBlow-up function as proposed in https://arxiv.org/abs/2210.00442 The blow-up order of the function is fixed to ensure C^2 regularity of the energies bands away from crossings and Lipschitz continuity at crossings.
DFTK.BlowupIdentity — TypeDefault blow-up corresponding to the standard kinetic energies.
DFTK.DielectricMixing — TypeWe use a simplification of the Resta model DOI 10.1103/physrevb.16.2717 and set $χ_0(q) = \frac{C_0 G^2}{4π (1 - C_0 G^2 / k_{TF}^2)}$ where $C_0 = 1 - ε_r$ with $ε_r$ being the macroscopic relative permittivity. We neglect $K_\text{xc}$, such that $J^{-1} ≈ \frac{k_{TF}^2 - C_0 G^2}{ε_r k_{TF}^2 - C_0 G^2}$
By default it assumes a relative permittivity of 10 (similar to Silicon). εr == 1 is equal to SimpleMixing and εr == Inf to KerkerMixing. The mixing is applied to $ρ$ and $ρ_\text{spin}$ in the same way.
DFTK.DielectricModel — TypeA localised dielectric model for $χ_0$:
\[\sqrt{L(x)} \text{IFFT} \frac{C_0 G^2}{4π (1 - C_0 G^2 / k_{TF}^2)} \text{FFT} \sqrt{L(x)}\]
where $C_0 = 1 - ε_r$, L(r) is a real-space localization function and otherwise the same conventions are used as in DielectricMixing.
DFTK.DivAgradOperator — TypeNonlocal "divAgrad" operator $-½ ∇ ⋅ (A ∇)$ where $A$ is a scalar field on the real-space grid. The $-½$ is included, such that this operator is a generalisation of the kinetic energy operator (which is obtained for $A=1$).
DFTK.ElementCohenBergstresser — MethodElementCohenBergstresser(
+API reference · DFTK.jl API reference
This page provides a plain list of all documented functions, structs, modules and macros in DFTK. Note that this list is neither structured, complete nor particularly clean, so it only provides rough orientation at the moment. The best reference is the code itself.
DFTK.timer — ConstantTimerOutput object used to store DFTK timings.
sourceDFTK.AbstractArchitecture — TypeAbstract supertype for architectures supported by DFTK.
sourceDFTK.AdaptiveBands — TypeDynamically adapt number of bands to be converged to ensure that the orbitals of lowest occupation are occupied to at most occupation_threshold. To obtain rapid convergence of the eigensolver a gap between the eigenvalues of the last occupied orbital and the last computed (but not converged) orbital of gap_min is ensured.
sourceDFTK.AdaptiveDiagtol — TypeAlgorithm for the tolerance used for the next diagonalization. This function takes $|ρ_{\rm next} - ρ_{\rm in}|$ and multiplies it with ratio_ρdiff to get the next diagtol, ensuring additionally that the returned value is between diagtol_min and diagtol_max and never increases.
sourceDFTK.Applyχ0Model — TypeFull χ0 application, optionally dropping terms or disabling Sternheimer. All keyword arguments passed to apply_χ0.
sourceDFTK.AtomicLocal — TypeAtomic local potential defined by model.atoms.
sourceDFTK.AtomicNonlocal — TypeNonlocal term coming from norm-conserving pseudopotentials in Kleinmann-Bylander form. $\text{Energy} = ∑_a ∑_{ij} ∑_{n} f_n \braket{ψ_n}{{\rm proj}_{ai}} D_{ij} \braket{{\rm proj}_{aj}}{ψ_n}.$
sourceDFTK.BlowupAbinit — TypeBlow-up function as used in Abinit.
sourceDFTK.BlowupCHV — TypeBlow-up function as proposed in arXiv:2210.00442. The blow-up order of the function is fixed to ensure C^2 regularity of the energies bands away from crossings and Lipschitz continuity at crossings.
sourceDFTK.BlowupIdentity — TypeDefault blow-up corresponding to the standard kinetic energies.
sourceDFTK.DFTKCalculator — MethodDFTKCalculator(
+ params::DFTK.DFTKParameters
+) -> DFTKCalculator
+
Construct a AtomsCalculators compatible calculator for DFTK. The model_kwargs are passed onto the Model constructor, the basis_kwargs to the PlaneWaveBasis constructor, the scf_kwargs to self_consistent_field. At the very least the DFT functionals and the Ecut needs to be specified.
By default the calculator preserves the symmetries that are stored inside the state (the basis is re-built, but symmetries are fixed and not re-computed).
Example
julia> DFTKCalculator(; model_kwargs=(; functionals=[:lda_x, :lda_c_vwn]),
+ basis_kwargs=(; Ecut=10, kgrid=(2, 2, 2)),
+ scf_kwargs=(; tol=1e-4))
sourceDFTK.DielectricMixing — TypeWe use a simplification of the Resta model and set $χ_0(q) = \frac{C_0 G^2}{4π (1 - C_0 G^2 / k_{TF}^2)}$ where $C_0 = 1 - ε_r$ with $ε_r$ being the macroscopic relative permittivity. We neglect $K_\text{xc}$, such that $J^{-1} ≈ \frac{k_{TF}^2 - C_0 G^2}{ε_r k_{TF}^2 - C_0 G^2}$
By default it assumes a relative permittivity of 10 (similar to Silicon). εr == 1 is equal to SimpleMixing and εr == Inf to KerkerMixing. The mixing is applied to $ρ$ and $ρ_\text{spin}$ in the same way.
sourceDFTK.DielectricModel — TypeA localised dielectric model for $χ_0$:
\[\sqrt{L(x)} \text{IFFT} \frac{C_0 G^2}{4π (1 - C_0 G^2 / k_{TF}^2)} \text{FFT} \sqrt{L(x)}\]
where $C_0 = 1 - ε_r$, L(r) is a real-space localization function and otherwise the same conventions are used as in DielectricMixing.
sourceDFTK.DivAgradOperator — TypeNonlocal "divAgrad" operator $-½ ∇ ⋅ (A ∇)$ where $A$ is a scalar field on the real-space grid. The $-½$ is included, such that this operator is a generalisation of the kinetic energy operator (which is obtained for $A=1$).
sourceDFTK.ElementCohenBergstresser — MethodElementCohenBergstresser(
key;
lattice_constant
) -> ElementCohenBergstresser
-
Element where the interaction with electrons is modelled as in CohenBergstresser1966. Only the homonuclear lattices of the diamond structure are implemented (i.e. Si, Ge, Sn).
key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.ElementCoulomb — MethodElementCoulomb(key; mass) -> ElementCoulomb
-
Element interacting with electrons via a bare Coulomb potential (for all-electron calculations) key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.ElementGaussian — MethodElementGaussian(α, L; symbol) -> ElementGaussian
-
Element interacting with electrons via a Gaussian potential. Symbol is non-mandatory.
sourceDFTK.ElementPsp — MethodElementPsp(key; psp, mass)
-
Element interacting with electrons via a pseudopotential model. key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.Energies — TypeA simple struct to contain a vector of energies, and utilities to print them in a nice format.
sourceDFTK.Entropy — TypeEntropy term -TS, where S is the electronic entropy. Turns the energy E into the free energy F=E-TS. This is in particular useful because the free energy, not the energy, is minimized at self-consistency.
sourceDFTK.Ewald — TypeEwald term: electrostatic energy per unit cell of the array of point charges defined by model.atoms in a uniform background of compensating charge yielding net neutrality.
sourceDFTK.ExplicitKpoints — TypeExplicitly define the k-points along which to perform BZ sampling. (Useful for bandstructure calculations)
sourceDFTK.ExternalFromFourier — TypeExternal potential from the (unnormalized) Fourier coefficients V(G) G is passed in cartesian coordinates
sourceDFTK.ExternalFromReal — TypeExternal potential from an analytic function V (in cartesian coordinates). No low-pass filtering is performed.
sourceDFTK.ExternalFromValues — TypeExternal potential given as values.
sourceDFTK.FermiTwoStage — TypeTwo-stage Fermi level finding algorithm starting from a Gaussian-smearing guess.
sourceDFTK.FixedBands — TypeIn each SCF step converge exactly n_bands_converge, computing along the way exactly n_bands_compute (usually a few more to ease convergence in systems with small gaps).
sourceDFTK.FourierMultiplication — TypeFourier space multiplication, like a kinetic energy term: (Hψ)(G) = multiplier(G) ψ(G).
sourceDFTK.GPU — MethodConstruct a particular GPU architecture by passing the ArrayType
sourceDFTK.GaussianWannierProjection — TypeA Gaussian-shaped initial guess. Can be used as an approximation of an s- or σ-like orbital.
sourceDFTK.Hartree — TypeHartree term: for a decaying potential V the energy would be
1/2 ∫ρ(x)ρ(y)V(x-y) dxdy
with the integral on x in the unit cell and of y in the whole space. For the Coulomb potential with periodic boundary conditions, this is rather
1/2 ∫ρ(x)ρ(y) G(x-y) dx dy
where G is the Green's function of the periodic Laplacian with zero mean (-Δ G = sum{R} 4π δR, integral of G zero on a unit cell).
sourceDFTK.HydrogenicWannierProjection — TypeA hydrogenic initial guess.
α is the diffusivity, $\frac{Z}/{a}$ where $Z$ is the atomic number and $a$ is the Bohr radius.
sourceDFTK.KerkerDosMixing — TypeThe same as KerkerMixing, but the Thomas-Fermi wavevector is computed from the current density of states at the Fermi level.
sourceDFTK.KerkerMixing — TypeKerker mixing: $J^{-1} ≈ \frac{|G|^2}{k_{TF}^2 + |G|^2}$ where $k_{TF}$ is the Thomas-Fermi wave vector. For spin-polarized calculations by default the spin density is not preconditioned. Unless a non-default value for $ΔDOS_Ω$ is specified. This value should roughly be the expected difference in density of states (per unit volume) between spin-up and spin-down.
Notes:
- Abinit calls $1/k_{TF}$ the dielectric screening length (parameter dielng)
sourceDFTK.Kinetic — TypeKinetic energy: 1/2 sumn fn ∫ |∇ψn|^2 * blowup(-i∇Ψ).
sourceDFTK.Kpoint — TypeDiscretization information for $k$-point-dependent quantities such as orbitals. More generally, a $k$-point is a block of the Hamiltonian; eg collinear spin is treated by doubling the number of kpoints.
sourceDFTK.LazyHcat — TypeSimple wrapper to represent a matrix formed by the concatenation of column blocks: it is mostly equivalent to hcat, but doesn't allocate the full matrix. LazyHcat only supports a few multiplication routines: furthermore, a multiplication involving this structure will always yield a plain array (and not a LazyHcat structure). LazyHcat is a lightweight subset of BlockArrays.jl's functionalities, but has the advantage to be able to store GPU Arrays (BlockArrays is heavily built on Julia's CPU Array).
sourceDFTK.LdosModel — TypeRepresents the LDOS-based $χ_0$ model
\[χ_0(r, r') = (-D_\text{loc}(r) δ(r, r') + D_\text{loc}(r) D_\text{loc}(r') / D)\]
where $D_\text{loc}$ is the local density of states and $D$ the density of states. For details see Herbst, Levitt 2020 arXiv:2009.01665
sourceDFTK.LibxcDensities — MethodLibxcDensities(
+
Element where the interaction with electrons is modelled as in CohenBergstresser1966. Only the homonuclear lattices of the diamond structure are implemented (i.e. Si, Ge, Sn).
key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.ElementCoulomb — MethodElementCoulomb(key; mass) -> ElementCoulomb
+
Element interacting with electrons via a bare Coulomb potential (for all-electron calculations) key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.ElementGaussian — MethodElementGaussian(α, L; symbol) -> ElementGaussian
+
Element interacting with electrons via a Gaussian potential. Symbol is non-mandatory.
sourceDFTK.ElementPsp — MethodElementPsp(key; psp, mass)
+
Element interacting with electrons via a pseudopotential model. key may be an element symbol (like :Si), an atomic number (e.g. 14) or an element name (e.g. "silicon")
sourceDFTK.Energies — TypeA simple struct to contain a vector of energies, and utilities to print them in a nice format.
sourceDFTK.Entropy — TypeEntropy term $-TS$, where $S$ is the electronic entropy. Turns the energy $E$ into the free energy $F=E-TS$. This is in particular useful because the free energy, not the energy, is minimized at self-consistency.
sourceDFTK.Ewald — TypeEwald term: electrostatic energy per unit cell of the array of point charges defined by model.atoms in a uniform background of compensating charge yielding net neutrality.
sourceDFTK.ExplicitKpoints — TypeExplicitly define the k-points along which to perform BZ sampling. (Useful for bandstructure calculations)
sourceDFTK.ExternalFromFourier — TypeExternal potential from the (unnormalized) Fourier coefficients V(G) G is passed in cartesian coordinates
sourceDFTK.ExternalFromReal — TypeExternal potential from an analytic function V (in cartesian coordinates). No low-pass filtering is performed.
sourceDFTK.ExternalFromValues — TypeExternal potential given as values.
sourceDFTK.FermiTwoStage — TypeTwo-stage Fermi level finding algorithm starting from a Gaussian-smearing guess.
sourceDFTK.FixedBands — TypeIn each SCF step converge exactly n_bands_converge, computing along the way exactly n_bands_compute (usually a few more to ease convergence in systems with small gaps).
sourceDFTK.FourierMultiplication — TypeFourier space multiplication, like a kinetic energy term:
\[(Hψ)(G) = {\rm multiplier}(G) ψ(G).\]
sourceDFTK.GPU — MethodConstruct a particular GPU architecture by passing the ArrayType
sourceDFTK.GaussianWannierProjection — TypeA Gaussian-shaped initial guess. Can be used as an approximation of an s- or σ-like orbital.
sourceDFTK.Hartree — TypeHartree term: for a decaying potential V the energy would be
\[1/2 ∫ρ(x)ρ(y)V(x-y) dxdy,\]
with the integral on x in the unit cell and of y in the whole space. For the Coulomb potential with periodic boundary conditions, this is rather
\[1/2 ∫ρ(x)ρ(y) G(x-y) dx dy,\]
where G is the Green's function of the periodic Laplacian with zero mean ($-Δ G = ∑_R 4π δ_R$, integral of G zero on a unit cell).
sourceDFTK.HydrogenicWannierProjection — TypeA hydrogenic initial guess.
α is the diffusivity, $\frac{Z}{a}$ where $Z$ is the atomic number and $a$ is the Bohr radius.
sourceDFTK.KerkerDosMixing — TypeThe same as KerkerMixing, but the Thomas-Fermi wavevector is computed from the current density of states at the Fermi level.
sourceDFTK.KerkerMixing — TypeKerker mixing: $J^{-1} ≈ \frac{|G|^2}{k_{TF}^2 + |G|^2}$ where $k_{TF}$ is the Thomas-Fermi wave vector. For spin-polarized calculations by default the spin density is not preconditioned. Unless a non-default value for $ΔDOS_Ω$ is specified. This value should roughly be the expected difference in density of states (per unit volume) between spin-up and spin-down.
Notes:
- Abinit calls $1/k_{TF}$ the dielectric screening length (parameter dielng)
sourceDFTK.Kinetic — TypeKinetic energy:
\[1/2 ∑_n f_n ∫ |∇ψ_n|^2 * {\rm blowup}(-i∇Ψ_n).\]
sourceDFTK.Kpoint — TypeDiscretization information for $k$-point-dependent quantities such as orbitals. More generally, a $k$-point is a block of the Hamiltonian; eg collinear spin is treated by doubling the number of kpoints.
sourceDFTK.LazyHcat — TypeSimple wrapper to represent a matrix formed by the concatenation of column blocks: it is mostly equivalent to hcat, but doesn't allocate the full matrix. LazyHcat only supports a few multiplication routines: furthermore, a multiplication involving this structure will always yield a plain array (and not a LazyHcat structure). LazyHcat is a lightweight subset of BlockArrays.jl's functionalities, but has the advantage to be able to store GPU Arrays (BlockArrays is heavily built on Julia's CPU Array).
sourceDFTK.LdosModel — TypeRepresents the LDOS-based $χ_0$ model
\[χ_0(r, r') = (-D_\text{loc}(r) δ(r, r') + D_\text{loc}(r) D_\text{loc}(r') / D)\]
where $D_\text{loc}$ is the local density of states and $D$ the density of states. For details see Herbst, Levitt 2020.
sourceDFTK.LibxcDensities — MethodLibxcDensities(
basis,
max_derivative::Integer,
ρ,
τ
) -> DFTK.LibxcDensities
-
Compute density in real space and its derivatives starting from ρ
sourceDFTK.LocalNonlinearity — TypeLocal nonlinearity, with energy ∫f(ρ) where ρ is the density
sourceDFTK.Magnetic — TypeMagnetic term $A⋅(-i∇)$. It is assumed (but not checked) that $∇⋅A = 0$.
sourceDFTK.MagneticFieldOperator — TypeMagnetic field operator A⋅(-i∇).
sourceDFTK.Model — MethodModel(system::AbstractSystem; kwargs...)
AtomsBase-compatible Model constructor. Sets structural information (atoms, positions, lattice, n_electrons etc.) from the passed system.
sourceDFTK.Model — MethodModel(lattice, atoms, positions; n_electrons, magnetic_moments, terms, temperature,
- smearing, spin_polarization, symmetries)
Creates the physical specification of a model (without any discretization information).
n_electrons is taken from atoms if not specified.
spin_polarization is :none by default (paired electrons) unless any of the elements has a non-zero initial magnetic moment. In this case the spin_polarization will be :collinear.
magnetic_moments is only used to determine the symmetry and the spin_polarization; it is not stored inside the datastructure.
smearing is Fermi-Dirac if temperature is non-zero, none otherwise
The symmetries kwarg allows (a) to pass true / false to enable / disable the automatic determination of lattice symmetries or (b) to pass an explicit list of symmetry operations to use for lowering the computational effort. The default behaviour is equal to true, namely that the code checks the specified model in form of the Hamiltonian terms, lattice, atoms and magnetic_moments parameters and from these automatically determines a set of symmetries it can safely use. If you want to pass custom symmetry operations (e.g. a reduced or extended set) use the symmetry_operations function. Notice that this may lead to wrong results if e.g. the external potential breaks some of the passed symmetries. Use false to turn off symmetries completely.
sourceDFTK.Model — MethodModel(model; [lattice, positions, atoms, kwargs...])
-Model{T}(model; [lattice, positions, atoms, kwargs...])
Construct an identical model to model with the option to change some of the contained parameters. This constructor is useful for changing the data type in the model or for changing lattice or positions in geometry/lattice optimisations.
sourceDFTK.MonkhorstPack — TypePerform BZ sampling employing a Monkhorst-Pack grid.
sourceDFTK.NbandsAlgorithm — TypeNbandsAlgorithm subtypes determine how many bands to compute and converge in each SCF step.
sourceDFTK.NonlocalOperator — TypeNonlocal operator in Fourier space in Kleinman-Bylander format, defined by its projectors P matrix and coupling terms D: Hψ = PDP' ψ.
sourceDFTK.NoopOperator — TypeNoop operation: don't do anything. Useful for energy terms that don't depend on the orbitals at all (eg nuclei-nuclei interaction).
sourceDFTK.PairwisePotential — MethodPairwisePotential(
+
Compute density in real space and its derivatives starting from ρ
sourceDFTK.LocalNonlinearity — TypeLocal nonlinearity, with energy ∫f(ρ) where ρ is the density
sourceDFTK.Magnetic — TypeMagnetic term $A⋅(-i∇)$. It is assumed (but not checked) that $∇⋅A = 0$.
sourceDFTK.MagneticFieldOperator — TypeMagnetic field operator A⋅(-i∇).
sourceDFTK.Model — MethodModel(system::AbstractSystem; kwargs...)
AtomsBase-compatible Model constructor. Sets structural information (atoms, positions, lattice, n_electrons etc.) from the passed system.
sourceDFTK.Model — MethodModel(lattice, atoms, positions; n_electrons, magnetic_moments, terms, temperature,
+ smearing, spin_polarization, symmetries)
Creates the physical specification of a model (without any discretization information).
n_electrons is taken from atoms if not specified.
spin_polarization is :none by default (paired electrons) unless any of the elements has a non-zero initial magnetic moment. In this case the spin_polarization will be :collinear.
magnetic_moments is only used to determine the symmetry and the spin_polarization; it is not stored inside the datastructure.
smearing is Fermi-Dirac if temperature is non-zero, none otherwise
The symmetries kwarg allows (a) to pass true / false to enable / disable the automatic determination of lattice symmetries or (b) to pass an explicit list of symmetry operations to use for lowering the computational effort. The default behaviour is equal to true, namely that the code checks the specified model in form of the Hamiltonian terms, lattice, atoms and magnetic_moments parameters and from these automatically determines a set of symmetries it can safely use. If you want to pass custom symmetry operations (e.g. a reduced or extended set) use the symmetry_operations function. Notice that this may lead to wrong results if e.g. the external potential breaks some of the passed symmetries. Use false to turn off symmetries completely.
sourceDFTK.Model — MethodModel(model; [lattice, positions, atoms, kwargs...])
+Model{T}(model; [lattice, positions, atoms, kwargs...])
Construct an identical model to model with the option to change some of the contained parameters. This constructor is useful for changing the data type in the model or for changing lattice or positions in geometry/lattice optimisations.
sourceDFTK.MonkhorstPack — TypePerform BZ sampling employing a Monkhorst-Pack grid.
sourceDFTK.NbandsAlgorithm — TypeNbandsAlgorithm subtypes determine how many bands to compute and converge in each SCF step.
sourceDFTK.NonlocalOperator — TypeNonlocal operator in Fourier space in Kleinman-Bylander format, defined by its projectors P matrix and coupling terms D: Hψ = PDP' ψ.
sourceDFTK.NoopOperator — TypeNoop operation: don't do anything. Useful for energy terms that don't depend on the orbitals at all (eg nuclei-nuclei interaction).
sourceDFTK.PairwisePotential — MethodPairwisePotential(
V,
params;
max_radius
) -> PairwisePotential
-
Pairwise terms: Pairwise potential between nuclei, e.g., Van der Waals potentials, such as Lennard—Jones terms. The potential is dependent on the distance between to atomic positions and the pairwise atomic types: For a distance d between to atoms A and B, the potential is V(d, params[(A, B)]). The parameters max_radius is of 100 by default, and gives the maximum distance (in Cartesian coordinates) between nuclei for which we consider interactions.
sourceDFTK.PlaneWaveBasis — TypeA plane-wave discretized Model. Normalization conventions:
- Things that are expressed in the G basis are normalized so that if $x$ is the vector, then the actual function is $\sum_G x_G e_G$ with $e_G(x) = e^{iG x} / \sqrt(\Omega)$, where $\Omega$ is the unit cell volume. This is so that, eg $norm(ψ) = 1$ gives the correct normalization. This also holds for the density and the potentials.
- Quantities expressed on the real-space grid are in actual values.
ifft and fft convert between these representations.
sourceDFTK.PlaneWaveBasis — MethodCreates a new basis identical to basis, but with a new k-point grid, e.g. an MonkhorstPack or a ExplicitKpoints grid.
sourceDFTK.PlaneWaveBasis — MethodCreates a PlaneWaveBasis using the kinetic energy cutoff Ecut and a k-point grid. By default a MonkhorstPack grid is employed, which can be specified as a MonkhorstPack object or by simply passing a vector of three integers as the kgrid. Optionally kshift allows to specify a shift (0 or 1/2 in each direction). If not specified a grid is generated using kgrid_from_maximal_spacing with a maximal spacing of 2π * 0.022 per Bohr.
sourceDFTK.PreconditionerNone — TypeNo preconditioning
sourceDFTK.PreconditionerTPA — Type(simplified version of) Tetter-Payne-Allan preconditioning ↑ M.P. Teter, M.C. Payne and D.C. Allan, Phys. Rev. B 40, 12255 (1989).
sourceDFTK.PspCorrection — TypePseudopotential correction energy. TODO discuss the need for this.
sourceDFTK.PspHgh — MethodPspHgh(path[, identifier, description])
Construct a Hartwigsen, Goedecker, Teter, Hutter separable dual-space Gaussian pseudopotential (1998) from file.
sourceDFTK.PspUpf — MethodPspUpf(path[, identifier])
Construct a Unified Pseudopotential Format pseudopotential from file.
Does not support:
- Fully-realtivistic / spin-orbit pseudos
- Bare Coulomb / all-electron potentials
- Semilocal potentials
- Ultrasoft potentials
- Projector-augmented wave potentials
- GIPAW reconstruction data
sourceDFTK.RealFourierOperator — TypeLinear operators that act on tuples (real, fourier) The main entry point is apply!(out, op, in) which performs the operation out += op*in where out and in are named tuples (real, fourier) They also implement mul! and Matrix(op) for exploratory use.
sourceDFTK.RealSpaceMultiplication — TypeReal space multiplication by a potential: (Hψ)(r) = V(r) ψ(r).
sourceDFTK.SimpleMixing — TypeSimple mixing: $J^{-1} ≈ 1$
sourceDFTK.TermNoop — TypeA term with a constant zero energy.
sourceDFTK.Xc — TypeExchange-correlation term, defined by a list of functionals and usually evaluated through libxc.
sourceDFTK.χ0Mixing — TypeGeneric mixing function using a model for the susceptibility composed of the sum of the χ0terms. For valid χ0terms See the subtypes of χ0Model. The dielectric model is solved in real space using a GMRES. Either the full kernel (RPA=false) or only the Hartree kernel (RPA=true) are employed. verbose=true lets the GMRES run in verbose mode (useful for debugging).
sourceAbstractFFTs.fft! — Methodfft!(
+
Pairwise terms: Pairwise potential between nuclei, e.g., Van der Waals potentials, such as Lennard—Jones terms. The potential is dependent on the distance between to atomic positions and the pairwise atomic types: For a distance d between to atoms A and B, the potential is V(d, params[(A, B)]). The parameters max_radius is of 100 by default, and gives the maximum distance (in Cartesian coordinates) between nuclei for which we consider interactions.
sourceDFTK.PlaneWaveBasis — TypeA plane-wave discretized Model. Normalization conventions:
- Things that are expressed in the G basis are normalized so that if $x$ is the vector, then the actual function is $\sum_G x_G e_G$ with $e_G(x) = e^{iG x} / \sqrt(\Omega)$, where $\Omega$ is the unit cell volume. This is so that, eg $norm(ψ) = 1$ gives the correct normalization. This also holds for the density and the potentials.
- Quantities expressed on the real-space grid are in actual values.
ifft and fft convert between these representations.
sourceDFTK.PlaneWaveBasis — MethodCreates a new basis identical to basis, but with a new k-point grid, e.g. an MonkhorstPack or a ExplicitKpoints grid.
sourceDFTK.PlaneWaveBasis — MethodCreates a PlaneWaveBasis using the kinetic energy cutoff Ecut and a k-point grid. By default a MonkhorstPack grid is employed, which can be specified as a MonkhorstPack object or by simply passing a vector of three integers as the kgrid. Optionally kshift allows to specify a shift (0 or 1/2 in each direction). If not specified a grid is generated using kgrid_from_maximal_spacing with a maximal spacing of 2π * 0.022 per Bohr.
sourceDFTK.PreconditionerNone — TypeNo preconditioning.
sourceDFTK.PreconditionerTPA — Type(Simplified version of) Tetter-Payne-Allan preconditioning.
sourceDFTK.PspCorrection — TypePseudopotential correction energy. TODO discuss the need for this.
sourceDFTK.PspHgh — MethodPspHgh(path[, identifier, description])
Construct a Hartwigsen, Goedecker, Teter, Hutter separable dual-space Gaussian pseudopotential (1998) from file.
sourceDFTK.PspUpf — MethodPspUpf(path[, identifier])
Construct a Unified Pseudopotential Format pseudopotential from file.
Does not support:
- Fully-realtivistic / spin-orbit pseudos
- Bare Coulomb / all-electron potentials
- Semilocal potentials
- Ultrasoft potentials
- Projector-augmented wave potentials
- GIPAW reconstruction data
sourceDFTK.RealFourierOperator — TypeLinear operators that act on tuples (real, fourier) The main entry point is apply!(out, op, in) which performs the operation out += op*in where out and in are named tuples (; real, fourier). They also implement mul! and Matrix(op) for exploratory use.
sourceDFTK.RealSpaceMultiplication — TypeReal space multiplication by a potential:
\[(Hψ)(r) = V(r) ψ(r).\]
sourceDFTK.ScfConvergenceDensity — TypeFlag convergence by using the L2Norm of the density change in one SCF step.
sourceDFTK.ScfConvergenceEnergy — TypeFlag convergence as soon as total energy change drops below a tolerance.
sourceDFTK.ScfConvergenceForce — TypeFlag convergence on the change in cartesian force between two iterations.
sourceDFTK.ScfDefaultCallback — TypeDefault callback function for self_consistent_field methods, which prints a convergence table.
sourceDFTK.ScfSaveCheckpoints — TypeAdds checkpointing to a DFTK self-consistent field calculation. The checkpointing file is silently overwritten. Requires the package for writing the output file (usually JLD2) to be loaded.
filename: Name of the checkpointing file.compress: Should compression be used on writing (rarely useful)save_ψ: Should the bands also be saved (noteworthy additional cost ... use carefully)
sourceDFTK.SimpleMixing — TypeSimple mixing: $J^{-1} ≈ 1$
sourceDFTK.TermNoop — TypeA term with a constant zero energy.
sourceDFTK.Xc — TypeExchange-correlation term, defined by a list of functionals and usually evaluated through libxc.
sourceDFTK.χ0Mixing — TypeGeneric mixing function using a model for the susceptibility composed of the sum of the χ0terms. For valid χ0terms See the subtypes of χ0Model. The dielectric model is solved in real space using a GMRES. Either the full kernel (RPA=false) or only the Hartree kernel (RPA=true) are employed. verbose=true lets the GMRES run in verbose mode (useful for debugging).
sourceAbstractFFTs.fft! — Methodfft!(
f_fourier::AbstractArray{T, 3} where T,
basis::PlaneWaveBasis,
f_real::AbstractArray{T, 3} where T
) -> Any
-
In-place version of fft!. NOTE: If kpt is given, not only f_fourier but also f_real is overwritten.
sourceAbstractFFTs.fft — Methodfft(
+
In-place version of fft!. NOTE: If kpt is given, not only f_fourier but also f_real is overwritten.
sourceAbstractFFTs.fft — Methodfft(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
f_real::AbstractArray{U}
) -> Any
-
fft(basis::PlaneWaveBasis, [kpt::Kpoint, ] f_real)
Perform an FFT to obtain the Fourier representation of f_real. If kpt is given, the coefficients are truncated to the k-dependent spherical basis set.
sourceAbstractFFTs.ifft! — Methodifft!(
+
fft(basis::PlaneWaveBasis, [kpt::Kpoint, ] f_real)
Perform an FFT to obtain the Fourier representation of f_real. If kpt is given, the coefficients are truncated to the k-dependent spherical basis set.
sourceAbstractFFTs.ifft! — Methodifft!(
f_real::AbstractArray{T, 3} where T,
basis::PlaneWaveBasis,
f_fourier::AbstractArray{T, 3} where T
) -> Any
-
In-place version of ifft.
sourceAbstractFFTs.ifft — Methodifft(basis::PlaneWaveBasis, f_fourier::AbstractArray) -> Any
-
ifft(basis::PlaneWaveBasis, [kpt::Kpoint, ] f_fourier)
Perform an iFFT to obtain the quantity defined by f_fourier defined on the k-dependent spherical basis set (if kpt is given) or the k-independent cubic (if it is not) on the real-space grid.
sourceAtomsBase.atomic_mass — Methodatomic_mass(el::DFTK.Element)
-
Return the atomic mass of an atom type
sourceAtomsBase.atomic_symbol — Methodatomic_symbol(_::DFTK.Element) -> Symbol
-
Chemical symbol corresponding to an element
sourceAtomsBase.atomic_system — Functionatomic_system(
+
In-place version of ifft.
sourceAbstractFFTs.ifft — Methodifft(basis::PlaneWaveBasis, f_fourier::AbstractArray) -> Any
+
ifft(basis::PlaneWaveBasis, [kpt::Kpoint, ] f_fourier)
Perform an iFFT to obtain the quantity defined by f_fourier defined on the k-dependent spherical basis set (if kpt is given) or the k-independent cubic (if it is not) on the real-space grid.
sourceAtomsBase.atomic_mass — Methodatomic_mass(el::DFTK.Element) -> Any
+
Return the atomic mass of an atom type
sourceAtomsBase.atomic_symbol — Methodatomic_symbol(_::DFTK.Element) -> Any
+
Chemical symbol corresponding to an element
sourceAtomsBase.atomic_system — Functionatomic_system(
lattice::AbstractMatrix{<:Number},
atoms::Vector{<:DFTK.Element},
positions::AbstractVector
@@ -48,26 +53,29 @@
magnetic_moments::AbstractVector
) -> AtomsBase.FlexibleSystem
atomic_system(model::DFTK.Model, magnetic_moments=[])
-atomic_system(lattice, atoms, positions, magnetic_moments=[])
Construct an AtomsBase atomic system from a DFTK model and associated magnetic moments or from the usual lattice, atoms and positions list used in DFTK plus magnetic moments.
sourceAtomsBase.periodic_system — Functionperiodic_system(model::Model) -> AtomsBase.FlexibleSystem
+atomic_system(lattice, atoms, positions, magnetic_moments=[])
Construct an AtomsBase atomic system from a DFTK model and associated magnetic moments or from the usual lattice, atoms and positions list used in DFTK plus magnetic moments.
sourceAtomsBase.periodic_system — Functionperiodic_system(model::Model) -> AtomsBase.FlexibleSystem
periodic_system(
model::Model,
magnetic_moments
) -> AtomsBase.FlexibleSystem
periodic_system(model::DFTK.Model, magnetic_moments=[])
-periodic_system(lattice, atoms, positions, magnetic_moments=[])
Construct an AtomsBase atomic system from a DFTK model and associated magnetic moments or from the usual lattice, atoms and positions list used in DFTK plus magnetic moments.
sourceBrillouin.KPaths.irrfbz_path — Functionirrfbz_path(model::Model) -> Brillouin.KPaths.KPath
+periodic_system(lattice, atoms, positions, magnetic_moments=[])
Construct an AtomsBase atomic system from a DFTK model and associated magnetic moments or from the usual lattice, atoms and positions list used in DFTK plus magnetic moments.
sourceBrillouin.KPaths.irrfbz_path — Functionirrfbz_path(
+ model::Model;
+ ...
+) -> Union{Brillouin.KPaths.KPath{3}, Brillouin.KPaths.KPath{2}, Brillouin.KPaths.KPath{1}}
irrfbz_path(
model::Model,
magnetic_moments;
dim,
space_group_number
-) -> Brillouin.KPaths.KPath
-
Extract the high-symmetry $k$-point path corresponding to the passed model using Brillouin. Uses the conventions described in the reference work by Cracknell, Davies, Miller, and Love (CDML). Of note, this has minor differences to the $k$-path reference (Y. Himuma et. al. Comput. Mater. Sci. 128, 140 (2017)) underlying the path-choices of Brillouin.jl, specifically for oA and mC Bravais types.
If the cell is a supercell of a smaller primitive cell, the standard $k$-path of the associated primitive cell is returned. So, the high-symmetry $k$ points are those of the primitive cell Brillouin zone, not those of the supercell Brillouin zone.
The dim argument allows to artificially truncate the dimension of the employed model, e.g. allowing to plot a 2D bandstructure of a 3D model (useful for example for plotting band structures of sheets with dim=2).
Due to lacking support in Spglib.jl for two-dimensional lattices it is (a) assumed that model.lattice is a conventional lattice and (b) required to pass the space group number using the space_group_number keyword argument.
sourceDFTK.CROP — FunctionCROP(
+) -> Union{Brillouin.KPaths.KPath{3}, Brillouin.KPaths.KPath{2}, Brillouin.KPaths.KPath{1}}
+
Extract the high-symmetry $k$-point path corresponding to the passed model using Brillouin. Uses the conventions described in the reference work by Cracknell, Davies, Miller, and Love (CDML). Of note, this has minor differences to the $k$-path reference (Y. Himuma et. al. Comput. Mater. Sci. 128, 140 (2017)) underlying the path-choices of Brillouin.jl, specifically for oA and mC Bravais types.
If the cell is a supercell of a smaller primitive cell, the standard $k$-path of the associated primitive cell is returned. So, the high-symmetry $k$ points are those of the primitive cell Brillouin zone, not those of the supercell Brillouin zone.
The dim argument allows to artificially truncate the dimension of the employed model, e.g. allowing to plot a 2D bandstructure of a 3D model (useful for example for plotting band structures of sheets with dim=2).
Due to lacking support in Spglib.jl for two-dimensional lattices it is (a) assumed that model.lattice is a conventional lattice and (b) required to pass the space group number using the space_group_number keyword argument.
sourceDFTK.CROP — FunctionCROP(
f,
x0,
m::Int64,
max_iter::Int64,
tol::Real
-) -> NamedTuple{(:fixpoint, :converged), _A} where _A<:Tuple{Any, Any}
+) -> NamedTuple{(:fixpoint, :converged), <:Tuple{Any, Any}}
CROP(
f,
x0,
@@ -75,25 +83,25 @@
max_iter::Int64,
tol::Real,
warming
-) -> NamedTuple{(:fixpoint, :converged), _A} where _A<:Tuple{Any, Any}
-
CROP-accelerated root-finding iteration for f, starting from x0 and keeping a history of m steps. Optionally warming specifies the number of non-accelerated steps to perform for warming up the history.
sourceDFTK.G_vectors — MethodG_vectors(
+) -> NamedTuple{(:fixpoint, :converged), <:Tuple{Any, Any}}
+
CROP-accelerated root-finding iteration for f, starting from x0 and keeping a history of m steps. Optionally warming specifies the number of non-accelerated steps to perform for warming up the history.
sourceDFTK.G_vectors — MethodG_vectors(
basis::PlaneWaveBasis
) -> AbstractArray{StaticArraysCore.SVector{3, Int64}, 3}
G_vectors(basis::PlaneWaveBasis)
-G_vectors(basis::PlaneWaveBasis, kpt::Kpoint)
The list of wave vectors $G$ in reduced (integer) coordinates of a basis or a $k$-point kpt.
sourceDFTK.G_vectors — MethodG_vectors(fft_size::Union{Tuple, AbstractVector}) -> Any
-
G_vectors([architecture=AbstractArchitecture], fft_size::Tuple)
The wave vectors G in reduced (integer) coordinates for a cubic basis set of given sizes.
sourceDFTK.G_vectors_cart — MethodG_vectors_cart(basis::PlaneWaveBasis) -> Any
+G_vectors(basis::PlaneWaveBasis, kpt::Kpoint)
The list of wave vectors $G$ in reduced (integer) coordinates of a basis or a $k$-point kpt.
sourceDFTK.G_vectors — MethodG_vectors(fft_size::Union{Tuple, AbstractVector}) -> Any
+
G_vectors(fft_size::Tuple)
The wave vectors G in reduced (integer) coordinates for a cubic basis set of given sizes.
sourceDFTK.G_vectors_cart — MethodG_vectors_cart(basis::PlaneWaveBasis) -> Any
G_vectors_cart(basis::PlaneWaveBasis)
-G_vectors_cart(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G$ vectors of a given basis or kpt, in cartesian coordinates.
sourceDFTK.Gplusk_vectors — MethodGplusk_vectors(basis::PlaneWaveBasis, kpt::Kpoint) -> Any
-
Gplusk_vectors(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G + k$ vectors, in reduced coordinates.
sourceDFTK.Gplusk_vectors_cart — MethodGplusk_vectors_cart(
+G_vectors_cart(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G$ vectors of a given basis or kpt, in cartesian coordinates.
sourceDFTK.Gplusk_vectors — MethodGplusk_vectors(basis::PlaneWaveBasis, kpt::Kpoint) -> Any
+
Gplusk_vectors(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G + k$ vectors, in reduced coordinates.
sourceDFTK.Gplusk_vectors_cart — MethodGplusk_vectors_cart(
basis::PlaneWaveBasis,
kpt::Kpoint
) -> Any
-
Gplusk_vectors_cart(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G + k$ vectors, in cartesian coordinates.
sourceDFTK.Gplusk_vectors_in_supercell — MethodGplusk_vectors_in_supercell(
+
Gplusk_vectors_cart(basis::PlaneWaveBasis, kpt::Kpoint)
The list of $G + k$ vectors, in cartesian coordinates.
sourceDFTK.Gplusk_vectors_in_supercell — MethodGplusk_vectors_in_supercell(
basis::PlaneWaveBasis,
basis_supercell::PlaneWaveBasis,
kpt::Kpoint
) -> Any
-
Maps all $k+G$ vectors of an given basis as $G$ vectors of the supercell basis, in reduced coordinates.
sourceDFTK.HybridMixing — MethodHybridMixing(
+
Maps all $k+G$ vectors of an given basis as $G$ vectors of the supercell basis, in reduced coordinates.
sourceDFTK.HybridMixing — MethodHybridMixing(
;
εr,
kTF,
@@ -104,62 +112,36 @@
The model for the susceptibility is
\[\begin{aligned}
χ_0(r, r') &= (-D_\text{loc}(r) δ(r, r') + D_\text{loc}(r) D_\text{loc}(r') / D) \\
&+ \sqrt{L(x)} \text{IFFT} \frac{C_0 G^2}{4π (1 - C_0 G^2 / k_{TF}^2)} \text{FFT} \sqrt{L(x)}
-\end{aligned}\]
where $C_0 = 1 - ε_r$, $D_\text{loc}$ is the local density of states, $D$ is the density of states and the same convention for parameters are used as in DielectricMixing. Additionally there is the real-space localization function L(r). For details see Herbst, Levitt 2020 arXiv:2009.01665
Important kwargs passed on to χ0Mixing
RPA: Is the random-phase approximation used for the kernel (i.e. only Hartree kernel is used and not XC kernel)verbose: Run the GMRES in verbose mode.reltol: Relative tolerance for GMRES
sourceDFTK.IncreaseMixingTemperature — MethodIncreaseMixingTemperature(
+\end{aligned}\]where $C_0 = 1 - ε_r$, $D_\text{loc}$ is the local density of states, $D$ is the density of states and the same convention for parameters are used as in DielectricMixing. Additionally there is the real-space localization function L(r). For details see Herbst, Levitt 2020.
Important kwargs passed on to χ0Mixing
RPA: Is the random-phase approximation used for the kernel (i.e. only Hartree kernel is used and not XC kernel)verbose: Run the GMRES in verbose mode.reltol: Relative tolerance for GMRES
sourceDFTK.IncreaseMixingTemperature — MethodIncreaseMixingTemperature(
;
factor,
above_ρdiff,
temperature_max
-) -> DFTK.var"#callback#643"{DFTK.var"#callback#642#644"{Int64, Float64}}
-
Increase the temperature used for computing the SCF preconditioners. Initially the temperature is increased by a factor, which is then smoothly lowered towards the temperature used within the model as the SCF converges. Once the density change is below above_ρdiff the mixing temperature is equal to the model temperature.
sourceDFTK.LdosMixing — MethodLdosMixing(; adjust_temperature, kwargs...) -> χ0Mixing
+) -> DFTK.var"#callback#688"{DFTK.var"#callback#687#689"{Int64, Float64}}
+
Increase the temperature used for computing the SCF preconditioners. Initially the temperature is increased by a factor, which is then smoothly lowered towards the temperature used within the model as the SCF converges. Once the density change is below above_ρdiff the mixing temperature is equal to the model temperature.
sourceDFTK.LdosMixing — MethodLdosMixing(; adjust_temperature, kwargs...) -> χ0Mixing
The model for the susceptibility is
\[\begin{aligned}
χ_0(r, r') &= (-D_\text{loc}(r) δ(r, r') + D_\text{loc}(r) D_\text{loc}(r') / D)
-\end{aligned}\]
where $D_\text{loc}$ is the local density of states, $D$ is the density of states. For details see Herbst, Levitt 2020 arXiv:2009.01665.
Important kwargs passed on to χ0Mixing
RPA: Is the random-phase approximation used for the kernel (i.e. only Hartree kernel is used and not XC kernel)verbose: Run the GMRES in verbose mode.reltol: Relative tolerance for GMRES
sourceDFTK.ScfAcceptImprovingStep — MethodScfAcceptImprovingStep(
+\end{aligned}\]where $D_\text{loc}$ is the local density of states, $D$ is the density of states. For details see Herbst, Levitt 2020.
Important kwargs passed on to χ0Mixing
RPA: Is the random-phase approximation used for the kernel (i.e. only Hartree kernel is used and not XC kernel)verbose: Run the GMRES in verbose mode.reltol: Relative tolerance for GMRES
sourceDFTK.ScfAcceptImprovingStep — MethodScfAcceptImprovingStep(
;
max_energy_change,
max_relative_residual
-) -> DFTK.var"#accept_step#735"{Float64, Float64}
-
Accept a step if the energy is at most increasing by max_energy and the residual is at most max_relative_residual times the residual in the previous step.
sourceDFTK.ScfConvergenceDensity — MethodScfConvergenceDensity(tolerance) -> DFTK.var"#689#690"
-
Flag convergence by using the L2Norm of the change between input density and unpreconditioned output density (ρout)
sourceDFTK.ScfConvergenceEnergy — MethodScfConvergenceEnergy(
- tolerance
-) -> DFTK.var"#is_converged#688"
-
Flag convergence as soon as total energy change drops below tolerance
sourceDFTK.ScfConvergenceForce — MethodScfConvergenceForce(
- tolerance
-) -> DFTK.var"#is_converged#691"
-
Flag convergence on the change in cartesian force between two iterations.
sourceDFTK.ScfDefaultCallback — MethodScfDefaultCallback(
-;
- show_damping,
- show_time
-) -> DFTK.var"#callback#685"{Bool, Bool}
-
Default callback function for self_consistent_field and newton, which prints a convergence table.
sourceDFTK.ScfDiagtol — MethodScfDiagtol(
-;
- ratio_ρdiff,
- diagtol_min,
- diagtol_max
-) -> DFTK.var"#determine_diagtol#693"{Float64}
-
Determine the tolerance used for the next diagonalization. This function takes $|ρnext - ρin|$ and multiplies it with ratio_ρdiff to get the next diagtol, ensuring additionally that the returned value is between diagtol_min and diagtol_max and never increases.
sourceDFTK.ScfPlotTrace — FunctionPlot the trace of an SCF, i.e. the absolute error of the total energy at each iteration versus the converged energy in a semilog plot. By default a new plot canvas is generated, but an existing one can be passed and reused along with kwargs for the call to plot!. Requires Plots to be loaded.
sourceDFTK.ScfSaveCheckpoints — FunctionScfSaveCheckpoints(
-
-) -> DFTK.var"#callback#680"{Bool, Bool, String}
-ScfSaveCheckpoints(
- filename;
- keep,
- overwrite
-) -> DFTK.var"#callback#680"{Bool, Bool}
-
Adds simplistic checkpointing to a DFTK self-consistent field calculation. Requires JLD2 to be loaded.
sourceDFTK.apply_K — Methodapply_K(basis::PlaneWaveBasis, δψ, ψ, ρ, occupation) -> Any
-
apply_K(basis::PlaneWaveBasis, δψ, ψ, ρ, occupation)
Compute the application of K defined at ψ to δψ. ρ is the density issued from ψ. δψ also generates a δρ, computed with compute_δρ.
sourceDFTK.apply_kernel — Methodapply_kernel(
+) -> DFTK.var"#accept_step#778"{Float64, Float64}
+
Accept a step if the energy is at most increasing by max_energy and the residual is at most max_relative_residual times the residual in the previous step.
sourceDFTK.apply_K — Methodapply_K(basis::PlaneWaveBasis, δψ, ψ, ρ, occupation) -> Any
+
apply_K(basis::PlaneWaveBasis, δψ, ψ, ρ, occupation)
Compute the application of K defined at ψ to δψ. ρ is the density issued from ψ. δψ also generates a δρ, computed with compute_δρ.
sourceDFTK.apply_kernel — Methodapply_kernel(
basis::PlaneWaveBasis,
δρ;
RPA,
kwargs...
) -> Any
-
apply_kernel(basis::PlaneWaveBasis, δρ; kwargs...)
Computes the potential response to a perturbation δρ in real space, as a 4D (i,j,k,σ) array.
sourceDFTK.apply_symop — Methodapply_symop(
+
apply_kernel(basis::PlaneWaveBasis, δρ; kwargs...)
Computes the potential response to a perturbation δρ in real space, as a 4D (i,j,k,σ) array.
sourceDFTK.apply_symop — Methodapply_symop(
symop::SymOp,
basis,
kpoint,
ψk::AbstractVecOrMat
) -> Tuple{Any, Any}
-
Apply a symmetry operation to eigenvectors ψk at a given kpoint to obtain an equivalent point in [-0.5, 0.5)^3 and associated eigenvectors (expressed in the basis of the new $k$-point).
sourceDFTK.apply_symop — Methodapply_symop(symop::SymOp, basis, ρin; kwargs...) -> Any
-
Apply a symmetry operation to a density.
sourceDFTK.apply_Ω — Methodapply_Ω(δψ, ψ, H::Hamiltonian, Λ) -> Any
-
apply_Ω(δψ, ψ, H::Hamiltonian, Λ)
Compute the application of Ω defined at ψ to δψ. H is the Hamiltonian computed from ψ and Λ is the set of Rayleigh coefficients ψk' * Hk * ψk at each k-point.
sourceDFTK.apply_χ0 — Methodapply_χ0(
+
Apply a symmetry operation to eigenvectors ψk at a given kpoint to obtain an equivalent point in [-0.5, 0.5)^3 and associated eigenvectors (expressed in the basis of the new $k$-point).
sourceDFTK.apply_symop — Methodapply_symop(symop::SymOp, basis, ρin; kwargs...) -> Any
+
Apply a symmetry operation to a density.
sourceDFTK.apply_Ω — Methodapply_Ω(δψ, ψ, H::Hamiltonian, Λ) -> Any
+
apply_Ω(δψ, ψ, H::Hamiltonian, Λ)
Compute the application of Ω defined at ψ to δψ. H is the Hamiltonian computed from ψ and Λ is the set of Rayleigh coefficients ψk' * Hk * ψk at each k-point.
sourceDFTK.apply_χ0 — Methodapply_χ0(
ham,
ψ,
occupation,
@@ -170,41 +152,45 @@
q,
kwargs_sternheimer...
) -> Any
-
Get the density variation δρ corresponding to a potential variation δV.
sourceDFTK.attach_psp — Methodattach_psp(
+
Get the density variation δρ corresponding to a potential variation δV.
sourceDFTK.attach_psp — Methodattach_psp(
system::AtomsBase.AbstractSystem,
pspmap::AbstractDict{Symbol, String}
) -> AtomsBase.FlexibleSystem
attach_psp(system::AbstractSystem, pspmap::AbstractDict{Symbol,String})
-attach_psp(system::AbstractSystem; psps::String...)
Return a new system with the pseudopotential property of all atoms set according to the passed pspmap, which maps from the atomic symbol to a pseudopotential identifier. Alternatively the mapping from atomic symbol to pseudopotential identifier can also be passed as keyword arguments. An empty string can be used to denote elements where the full Coulomb potential should be employed.
Examples
Select pseudopotentials for all silicon and oxygen atoms in the system.
julia> attach_psp(system, Dict(:Si => "hgh/lda/si-q4", :O => "hgh/lda/o-q6")
Same thing but using the kwargs syntax:
julia> attach_psp(system, Si="hgh/lda/si-q4", O="hgh/lda/o-q6")
sourceDFTK.band_data_to_dict — Methodband_data_to_dict(
- band_data::NamedTuple
-) -> Union{Nothing, Dict}
-
Convert a band computational result to a dictionary representation. Intended to give a condensed set of results and useful metadata for post processing. See also the todict function for the Model and the PlaneWaveBasis, which are called from this function and the outputs merged. Note, that only the master process returns the dictionary. On all other processors nothing is returned.
Some details on the conventions for the returned data:
- εF: Computed Fermi level (if present in band_data)
- labels: A mapping of high-symmetry k-Point labels to the index in the
"kcoords" vector of the corresponding k-Point. - eigenvalues, eigenvalueserror, occupation, residualnorms: (nspin, nkpoints, n_bands) arrays of the respective data.
- niter: (nspin, n_kpoints) array of the number of iterations the diagonalisation routine required.
sourceDFTK.build_fft_plans! — Methodbuild_fft_plans!(
+attach_psp(system::AbstractSystem; psps::String...)
Return a new system with the pseudopotential property of all atoms set according to the passed pspmap, which maps from the atomic symbol to a pseudopotential identifier. Alternatively the mapping from atomic symbol to pseudopotential identifier can also be passed as keyword arguments. An empty string can be used to denote elements where the full Coulomb potential should be employed.
Examples
Select pseudopotentials for all silicon and oxygen atoms in the system.
julia> attach_psp(system, Dict(:Si => "hgh/lda/si-q4", :O => "hgh/lda/o-q6")
Same thing but using the kwargs syntax:
julia> attach_psp(system, Si="hgh/lda/si-q4", O="hgh/lda/o-q6")
sourceDFTK.band_data_to_dict — Methodband_data_to_dict(
+ band_data::NamedTuple;
+ kwargs...
+) -> Dict{String, Any}
+
Convert a band computational result to a dictionary representation. Intended to give a condensed set of results and useful metadata for post processing. See also the todict function for the Model and the PlaneWaveBasis, which are called from this function and the outputs merged. Note, that only the master process returns meaningful data. All other processors still return a dictionary (to simplify code in calling locations), but the data may be dummy.
Some details on the conventions for the returned data:
εF: Computed Fermi level (if present in band_data)labels: A mapping of high-symmetry k-Point labels to the index in the "kcoords" vector of the corresponding k-Point.eigenvalues, eigenvalues_error, occupation, residual_norms: (n_bands, n_kpoints, n_spin) arrays of the respective data.n_iter: (n_kpoints, n_spin) array of the number of iterations the diagonalization routine required.kpt_max_n_G: Maximal number of G-vectors used for any k-point.kpt_n_G_vectors: (n_kpoints, n_spin) array, the number of valid G-vectors for each k-point, i.e. the extend along the first axis of ψ where data is valid.kpt_G_vectors: (3, max_n_G, n_kpoints, n_spin) array of the integer (reduced) coordinates of the G-points used for each k-point.ψ: (max_n_G, n_bands, n_kpoints, n_spin) arrays where max_n_G is the maximal number of G-vectors used for any k-point. The data is zero-padded, i.e. for k-points which have less G-vectors than maxnG, then there are tailing zeros.
sourceDFTK.build_fft_plans! — Methodbuild_fft_plans!(
tmp::Array{ComplexF64}
) -> Tuple{FFTW.cFFTWPlan{ComplexF64, -1, true}, FFTW.cFFTWPlan{ComplexF64, -1, false}, Any, Any}
-
Plan a FFT of type T and size fft_size, spending some time on finding an optimal algorithm. (Inplace, out-of-place) x (forward, backward) FFT plans are returned.
sourceDFTK.build_form_factors — Methodbuild_form_factors(psp, qs::Array) -> Matrix
-
Build form factors (Fourier transforms of projectors) for an atom centered at 0.
sourceDFTK.build_projection_vectors_ — Methodbuild_projection_vectors_(
+
Plan a FFT of type T and size fft_size, spending some time on finding an optimal algorithm. (Inplace, out-of-place) x (forward, backward) FFT plans are returned.
sourceDFTK.build_form_factors — Methodbuild_form_factors(
+ psp,
+ G_plus_k::AbstractArray{StaticArraysCore.SArray{Tuple{3}, TT, 1, 3}, 1}
+) -> Matrix{T} where T<:(Complex{_A} where _A)
+
Build form factors (Fourier transforms of projectors) for an atom centered at 0.
sourceDFTK.build_projection_vectors — Methodbuild_projection_vectors(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
kpt::Kpoint,
psps,
psp_positions
) -> Any
Build projection vectors for a atoms array generated by term_nonlocal
\[\begin{aligned}
-H_{\rm at} &= \sum_{ij} C_{ij} \ket{p_i} \bra{p_j} \\
-H_{\rm per} &= \sum_R \sum_{ij} C_{ij} \ket{p_i(x-R)} \bra{p_j(x-R)}
+H_{\rm at} &= \sum_{ij} C_{ij} \ket{{\rm proj}_i} \bra{{\rm proj}_j} \\
+H_{\rm per} &= \sum_R \sum_{ij} C_{ij} \ket{{\rm proj}_i(x-R)} \bra{{\rm proj}_j(x-R)}
\end{aligned}\]
\[\begin{aligned}
\braket{e_k(G') \middle| H_{\rm per}}{e_k(G)}
&= \ldots \\
- &= \frac{1}{Ω} \sum_{ij} C_{ij} \hat p_i(k+G') \hat p_j^*(k+G),
-\end{aligned}\]
where $\hat p_i(q) = ∫_{ℝ^3} p_i(r) e^{-iq·r} dr$.
We store $\frac{1}{\sqrt Ω} \hat p_i(k+G)$ in proj_vectors.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(scfres::NamedTuple) -> Any
-
Transpose all data from a given self-consistent-field result from unit cell to supercell conventions. The parameters to adapt are the following:
basis_supercell and ψ_supercell are computed by the routines above.- The supercell occupations vector is the concatenation of all input occupations vectors.
- The supercell density is computed with supercell occupations and
ψ_supercell. - Supercell energies are the multiplication of input energies by the number of unit cells in the supercell.
Other parameters stay untouched.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(
+ &= \frac{1}{Ω} \sum_{ij} C_{ij} \widehat{\rm proj}_i(k+G') \widehat{\rm proj}_j^*(k+G),
+\end{aligned}\]where $\widehat{\rm proj}_i(p) = ∫_{ℝ^3} {\rm proj}_i(r) e^{-ip·r} dr$.
We store $\frac{1}{\sqrt Ω} \widehat{\rm proj}_i(k+G)$ in proj_vectors.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(scfres::NamedTuple) -> NamedTuple
+
Transpose all data from a given self-consistent-field result from unit cell to supercell conventions. The parameters to adapt are the following:
basis_supercell and ψ_supercell are computed by the routines above.- The supercell occupations vector is the concatenation of all input occupations vectors.
- The supercell density is computed with supercell occupations and
ψ_supercell. - Supercell energies are the multiplication of input energies by the number of unit cells in the supercell.
Other parameters stay untouched.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(
basis::PlaneWaveBasis{T, VT} where VT<:Real
-) -> PlaneWaveBasis
-
Construct a plane-wave basis whose unit cell is the supercell associated to an input basis $k$-grid. All other parameters are modified so that the respective physical systems associated to both basis are equivalent.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(
+) -> PlaneWaveBasis{T, _A, Arch, _B, _C} where {T<:Real, _A<:Real, Arch<:DFTK.AbstractArchitecture, _B<:AbstractArray{StaticArraysCore.SVector{3, Int64}, 3}, _C<:AbstractArray{StaticArraysCore.SVector{3, _A}, 3}}
+
Construct a plane-wave basis whose unit cell is the supercell associated to an input basis $k$-grid. All other parameters are modified so that the respective physical systems associated to both basis are equivalent.
sourceDFTK.cell_to_supercell — Methodcell_to_supercell(
ψ,
basis::PlaneWaveBasis{T<:Real, VT} where VT<:Real,
basis_supercell::PlaneWaveBasis{T<:Real, VT} where VT<:Real
) -> Any
-
Re-organize Bloch waves computed in a given basis as Bloch waves of the associated supercell basis. The output ψ_supercell have a single component at $Γ$-point, such that ψ_supercell[Γ][:, k+n] contains ψ[k][:, n], within normalization on the supercell.
sourceDFTK.cg! — Methodcg!(
+
Re-organize Bloch waves computed in a given basis as Bloch waves of the associated supercell basis. The output ψ_supercell have a single component at $Γ$-point, such that ψ_supercell[Γ][:, k+n] contains ψ[k][:, n], within normalization on the supercell.
sourceDFTK.cg! — Methodcg!(
x::AbstractArray{T, 1},
A::LinearMaps.LinearMap{T},
b::AbstractArray{T, 1};
@@ -214,30 +200,30 @@
tol,
maxiter,
miniter
-) -> NamedTuple{(:x, :converged, :tol, :residual_norm, :n_iter, :maxiter, :stage), _A} where _A<:Tuple{AbstractVector, Bool, Float64, Any, Int64, Int64, Symbol}
-
Implementation of the conjugate gradient method which allows for preconditioning and projection operations along iterations.
sourceDFTK.charge_ionic — Methodcharge_ionic(el::DFTK.Element) -> Int64
-
Return the total ionic charge of an atom type (nuclear charge - core electrons)
sourceDFTK.charge_nuclear — Methodcharge_nuclear(_::DFTK.Element) -> Int64
-
Return the total nuclear charge of an atom type
sourceDFTK.cis2pi — Methodcis2pi(x) -> Any
-
Function to compute exp(2π i x)
sourceDFTK.compute_amn_kpoint — Methodcompute_amn_kpoint(
+) -> NamedTuple{(:x, :converged, :tol, :residual_norm, :n_iter, :maxiter, :stage), <:Tuple{AbstractVector, Bool, Float64, Any, Int64, Int64, Symbol}}
+
Implementation of the conjugate gradient method which allows for preconditioning and projection operations along iterations.
sourceDFTK.charge_ionic — Methodcharge_ionic(el::DFTK.Element) -> Int64
+
Return the total ionic charge of an atom type (nuclear charge - core electrons)
sourceDFTK.charge_nuclear — Methodcharge_nuclear(_::DFTK.Element) -> Int64
+
Return the total nuclear charge of an atom type
sourceDFTK.cis2pi — Methodcis2pi(x) -> Any
+
Function to compute exp(2π i x)
sourceDFTK.compute_amn_kpoint — Methodcompute_amn_kpoint(
basis::PlaneWaveBasis,
kpt,
ψk,
projections,
n_bands
) -> Any
-
Compute the starting matrix for Wannierization.
Wannierization searches for a unitary matrix $U_{m_n}$. As a starting point for the search, we can provide an initial guess function $g$ for the shape of the Wannier functions, based on what we expect from knowledge of the problem or physical intuition. This starting matrix is called $[A_k]_{m,n}$, and is computed as follows: $[A_k]_{m,n} = \langle ψ_m^k | g^{\text{per}}_n \rangle$. The matrix will be orthonormalized by the chosen Wannier program, we don't need to do so ourselves.
Centers are to be given in lattice coordinates and G_vectors in reduced coordinates. The dot product is computed in the Fourier space.
Given an orbital $g_n$, the periodized orbital is defined by : $g^{per}_n = \sum\limits_{R \in {\rm lattice}} g_n( \cdot - R)$. The Fourier coefficient of $g^{per}_n$ at any G is given by the value of the Fourier transform of $g_n$ in G.
Each projection is a callable object that accepts the basis and some qpoints as an argument, and returns the Fourier transform of $g_n$ at the qpoints.
sourceDFTK.compute_bands — Methodcompute_bands(
+
Compute the starting matrix for Wannierization.
Wannierization searches for a unitary matrix $U_{m_n}$. As a starting point for the search, we can provide an initial guess function $g$ for the shape of the Wannier functions, based on what we expect from knowledge of the problem or physical intuition. This starting matrix is called $[A_k]_{m,n}$, and is computed as follows: $[A_k]_{m,n} = \langle ψ_m^k | g^{\text{per}}_n \rangle$. The matrix will be orthonormalized by the chosen Wannier program, we don't need to do so ourselves.
Centers are to be given in lattice coordinates and G_vectors in reduced coordinates. The dot product is computed in the Fourier space.
Given an orbital $g_n$, the periodized orbital is defined by : $g^{per}_n = \sum\limits_{R \in {\rm lattice}} g_n( \cdot - R)$. The Fourier coefficient of $g^{per}_n$ at any G is given by the value of the Fourier transform of $g_n$ in G.
Each projection is a callable object that accepts the basis and some p-points as an argument, and returns the Fourier transform of $g_n$ at the p-points.
sourceDFTK.compute_bands — Methodcompute_bands(
basis_or_scfres,
kpath::Brillouin.KPaths.KPath;
kline_density,
kwargs...
-) -> NamedTuple{(:basis, :ψ, :eigenvalues, :ρ, :εF, :occupation, :diagonalization, :kinter)}
-
Compute band data along a specific Brillouin.KPath using a kline_density, the number of $k$-points per inverse bohrs (i.e. overall in units of length).
If not given, the path is determined automatically by inspecting the Model. If you are using spin, you should pass the magnetic_moments as a kwarg to ensure these are taken into account when determining the path.
sourceDFTK.compute_bands — Methodcompute_bands(
+) -> NamedTuple
+
Compute band data along a specific Brillouin.KPath using a kline_density, the number of $k$-points per inverse bohrs (i.e. overall in units of length).
If not given, the path is determined automatically by inspecting the Model. If you are using spin, you should pass the magnetic_moments as a kwarg to ensure these are taken into account when determining the path.
sourceDFTK.compute_bands — Methodcompute_bands(
scfres::NamedTuple,
kgrid::DFTK.AbstractKgrid;
n_bands,
kwargs...
-) -> NamedTuple{(:basis, :ψ, :eigenvalues, :ρ, :εF, :occupation, :diagonalization), _A} where _A<:Tuple{PlaneWaveBasis, Any, Any, Any, Any, Any, Vector}
-
Compute band data starting from SCF results. εF and ρ from the scfres are forwarded to the band computation and n_bands is by default selected as n_bands_scf + 5sqrt(n_bands_scf).
sourceDFTK.compute_bands — Methodcompute_bands(
+) -> NamedTuple{(:basis, :ψ, :eigenvalues, :ρ, :εF, :occupation, :diagonalization), <:Tuple{PlaneWaveBasis{T, _A, Arch, _B, _C} where {T<:Real, _A<:Real, Arch<:DFTK.AbstractArchitecture, _B<:AbstractArray{StaticArraysCore.SVector{3, Int64}, 3}, _C<:AbstractArray{StaticArraysCore.SVector{3, _A}, 3}}, Any, Any, Any, Any, Any, Vector{T} where T<:NamedTuple}}
+
Compute band data starting from SCF results. εF and ρ from the scfres are forwarded to the band computation and n_bands is by default selected as n_bands_scf + 5sqrt(n_bands_scf).
sourceDFTK.compute_bands — Methodcompute_bands(
basis::PlaneWaveBasis,
kgrid::DFTK.AbstractKgrid;
n_bands,
@@ -247,26 +233,26 @@
eigensolver,
tol,
kwargs...
-) -> NamedTuple{(:basis, :ψ, :eigenvalues, :ρ, :εF, :occupation, :diagonalization), _A} where _A<:Tuple{PlaneWaveBasis, Any, Any, Any, Nothing, Nothing, Vector}
-
Compute n_bands eigenvalues and Bloch waves at the k-Points specified by the kgrid. All kwargs not specified below are passed to diagonalize_all_kblocks:
kgrid: A custom kgrid to perform the band computation, e.g. a new MonkhorstPack grid.tol The default tolerance for the eigensolver is substantially lower than for SCF computations. Increase if higher accuracy desired.eigensolver: The diagonalisation method to be employed.
sourceDFTK.compute_current — Methodcompute_current(
+) -> NamedTuple{(:basis, :ψ, :eigenvalues, :ρ, :εF, :occupation, :diagonalization), <:Tuple{PlaneWaveBasis{T, _A, Arch, _B, _C} where {T<:Real, _A<:Real, Arch<:DFTK.AbstractArchitecture, _B<:AbstractArray{StaticArraysCore.SVector{3, Int64}, 3}, _C<:AbstractArray{StaticArraysCore.SVector{3, _A}, 3}}, Any, Any, Any, Nothing, Nothing, Vector{T} where T<:NamedTuple}}
+
Compute n_bands eigenvalues and Bloch waves at the k-Points specified by the kgrid. All kwargs not specified below are passed to diagonalize_all_kblocks:
kgrid: A custom kgrid to perform the band computation, e.g. a new MonkhorstPack grid.tol The default tolerance for the eigensolver is substantially lower than for SCF computations. Increase if higher accuracy desired.eigensolver: The diagonalisation method to be employed.
sourceDFTK.compute_current — Methodcompute_current(
basis::PlaneWaveBasis,
ψ,
occupation
) -> Vector
-
Computes the probability (not charge) current, ∑ fn Im(ψn* ∇ψn)
sourceDFTK.compute_density — Methodcompute_density(
+
Computes the probability (not charge) current, $∑_n f_n \Im(ψ_n · ∇ψ_n)$.
sourceDFTK.compute_density — Methodcompute_density(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
ψ,
occupation;
occupation_threshold
) -> AbstractArray{_A, 4} where _A
-
compute_density(basis::PlaneWaveBasis, ψ::AbstractVector, occupation::AbstractVector)
Compute the density for a wave function ψ discretized on the plane-wave grid basis, where the individual k-points are occupied according to occupation. ψ should be one coefficient matrix per $k$-point. It is possible to ask only for occupations higher than a certain level to be computed by using an optional occupation_threshold. By default all occupation numbers are considered.
sourceDFTK.compute_dos — Methodcompute_dos(
+
compute_density(basis::PlaneWaveBasis, ψ::AbstractVector, occupation::AbstractVector)
Compute the density for a wave function ψ discretized on the plane-wave grid basis, where the individual k-points are occupied according to occupation. ψ should be one coefficient matrix per $k$-point. It is possible to ask only for occupations higher than a certain level to be computed by using an optional occupation_threshold. By default all occupation numbers are considered.
sourceDFTK.compute_dos — Methodcompute_dos(
ε,
basis,
eigenvalues;
smearing,
temperature
) -> Any
-
Total density of states at energy ε
sourceDFTK.compute_dynmat — Methodcompute_dynmat(
+
Total density of states at energy ε
sourceDFTK.compute_dynmat — Methodcompute_dynmat(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
ψ,
occupation;
@@ -277,15 +263,16 @@
eigenvalues,
kwargs...
) -> Any
-
Compute the dynamical matrix in the form of a $3×n_{\rm atoms}×3×n_{\rm atoms}$ tensor in reduced coordinates.
sourceDFTK.compute_dynmat_cart — Methodcompute_dynmat_cart(
+
Compute the dynamical matrix in the form of a $3×n_{\rm atoms}×3×n_{\rm atoms}$ tensor in reduced coordinates.
sourceDFTK.compute_dynmat_cart — Methodcompute_dynmat_cart(
basis::PlaneWaveBasis,
ψ,
occupation;
kwargs...
) -> Any
-
Cartesian form of compute_dynmat.
sourceDFTK.compute_fft_size — Methodcompute_fft_size(
+
Cartesian form of compute_dynmat.
sourceDFTK.compute_fft_size — Methodcompute_fft_size(
model::Model{T},
- Ecut
+ Ecut;
+ ...
) -> Tuple{Vararg{Any, _A}} where _A
compute_fft_size(
model::Model{T},
@@ -296,22 +283,22 @@
factors,
kwargs...
) -> Tuple{Vararg{Any, _A}} where _A
-
Determine the minimal grid size for the cubic basis set to be able to represent product of orbitals (with the default supersampling=2).
Optionally optimize the grid afterwards for the FFT procedure by ensuring factorization into small primes.
The function will determine the smallest parallelepiped containing the wave vectors $|G|^2/2 \leq E_\text{cut} ⋅ \text{supersampling}^2$. For an exact representation of the density resulting from wave functions represented in the spherical basis sets, supersampling should be at least 2.
If factors is not empty, ensure that the resulting fft_size contains all the factors
sourceDFTK.compute_forces — Methodcompute_forces(scfres) -> Any
-
Compute the forces of an obtained SCF solution. Returns the forces wrt. the fractional lattice vectors. To get cartesian forces use compute_forces_cart. Returns a list of lists of forces (as SVector{3}) in the same order as the atoms and positions in the underlying Model.
sourceDFTK.compute_forces_cart — Methodcompute_forces_cart(
+
Determine the minimal grid size for the cubic basis set to be able to represent product of orbitals (with the default supersampling=2).
Optionally optimize the grid afterwards for the FFT procedure by ensuring factorization into small primes.
The function will determine the smallest parallelepiped containing the wave vectors $|G|^2/2 \leq E_\text{cut} ⋅ \text{supersampling}^2$. For an exact representation of the density resulting from wave functions represented in the spherical basis sets, supersampling should be at least 2.
If factors is not empty, ensure that the resulting fft_size contains all the factors
sourceDFTK.compute_forces — Methodcompute_forces(scfres) -> Any
+
Compute the forces of an obtained SCF solution. Returns the forces wrt. the fractional lattice vectors. To get cartesian forces use compute_forces_cart. Returns a list of lists of forces (as SVector{3}) in the same order as the atoms and positions in the underlying Model.
sourceDFTK.compute_forces_cart — Methodcompute_forces_cart(
basis::PlaneWaveBasis,
ψ,
occupation;
kwargs...
) -> Any
-
Compute the cartesian forces of an obtained SCF solution in Hartree / Bohr. Returns a list of lists of forces [[force for atom in positions] for (element, positions) in atoms] which has the same structure as the atoms object passed to the underlying Model.
sourceDFTK.compute_inverse_lattice — Methodcompute_inverse_lattice(lattice::AbstractArray{T, 2}) -> Any
-
Compute the inverse of the lattice. Takes special care of 1D or 2D cases.
sourceDFTK.compute_kernel — Methodcompute_kernel(
+
Compute the cartesian forces of an obtained SCF solution in Hartree / Bohr. Returns a list of lists of forces [[force for atom in positions] for (element, positions) in atoms] which has the same structure as the atoms object passed to the underlying Model.
sourceDFTK.compute_inverse_lattice — Methodcompute_inverse_lattice(lattice::AbstractArray{T, 2}) -> Any
+
Compute the inverse of the lattice. Takes special care of 1D or 2D cases.
sourceDFTK.compute_kernel — Methodcompute_kernel(
basis::PlaneWaveBasis{T, VT} where VT<:Real;
kwargs...
) -> Any
compute_kernel(basis::PlaneWaveBasis; kwargs...)
Computes a matrix representation of the full response kernel (derivative of potential with respect to density) in real space. For non-spin-polarized calculations the matrix dimension is prod(basis.fft_size) × prod(basis.fft_size) and for collinear spin-polarized cases it is 2prod(basis.fft_size) × 2prod(basis.fft_size). In this case the matrix has effectively 4 blocks
\[\left(\begin{array}{cc}
K_{αα} & K_{αβ}\\
K_{βα} & K_{ββ}
-\end{array}\right)\]
sourceDFTK.compute_ldos — Methodcompute_ldos(
+\end{array}\right)\]
sourceDFTK.compute_ldos — Methodcompute_ldos(
ε,
basis::PlaneWaveBasis{T, VT} where VT<:Real,
eigenvalues,
@@ -320,17 +307,18 @@
temperature,
weight_threshold
) -> AbstractArray{_A, 4} where _A
-
Local density of states, in real space. weight_threshold is a threshold to screen away small contributions to the LDOS.
sourceDFTK.compute_occupation — Methodcompute_occupation(
+
Local density of states, in real space. weight_threshold is a threshold to screen away small contributions to the LDOS.
sourceDFTK.compute_occupation — Methodcompute_occupation(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
eigenvalues::AbstractVector,
εF::Number;
temperature,
smearing
-) -> NamedTuple{(:occupation, :εF), _A} where _A<:Tuple{Any, Number}
-
Compute occupation given eigenvalues and Fermi level
sourceDFTK.compute_occupation — Methodcompute_occupation(
+) -> NamedTuple{(:occupation, :εF), <:Tuple{Any, Number}}
+
Compute occupation given eigenvalues and Fermi level
sourceDFTK.compute_occupation — Methodcompute_occupation(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
- eigenvalues::AbstractVector
-) -> NamedTuple{(:occupation, :εF), _A} where _A<:Tuple{Any, Number}
+ eigenvalues::AbstractVector;
+ ...
+) -> NamedTuple{(:occupation, :εF), <:Tuple{Any, Number}}
compute_occupation(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
eigenvalues::AbstractVector,
@@ -338,44 +326,42 @@
tol_n_elec,
temperature,
smearing
-) -> NamedTuple{(:occupation, :εF), _A} where _A<:Tuple{Any, Number}
-
Compute occupation and Fermi level given eigenvalues and using fermialg. The tol_n_elec gives the accuracy on the electron count which should be at least achieved.
sourceDFTK.compute_recip_lattice — Methodcompute_recip_lattice(lattice::AbstractArray{T, 2}) -> Any
-
Compute the reciprocal lattice. We use the convention that the reciprocal lattice is the set of G vectors such that G ⋅ R ∈ 2π ℤ for all R in the lattice.
sourceDFTK.compute_stresses_cart — Methodcompute_stresses_cart(scfres) -> Any
-
Compute the stresses (= 1/Vol dE/d(M*lattice), taken at M=I) of an obtained SCF solution.
sourceDFTK.compute_transfer_matrix — Methodcompute_transfer_matrix(
- basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
+) -> NamedTuple{(:occupation, :εF), <:Tuple{Any, Number}}
+
Compute occupation and Fermi level given eigenvalues and using fermialg. The tol_n_elec gives the accuracy on the electron count which should be at least achieved.
sourceDFTK.compute_recip_lattice — Methodcompute_recip_lattice(lattice::AbstractArray{T, 2}) -> Any
+
Compute the reciprocal lattice. We use the convention that the reciprocal lattice is the set of G vectors such that G ⋅ R ∈ 2π ℤ for all R in the lattice.
sourceDFTK.compute_stresses_cart — Methodcompute_stresses_cart(scfres) -> Any
+
Compute the stresses of an obtained SCF solution. The stress tensor is given by
\[\left( \begin{array}{ccc}
+σ_{xx} σ_{xy} σ_{xz} \\
+σ_{yx} σ_{yy} σ_{yz} \\
+σ_{zx} σ_{zy} σ_{zz}
+\right) = \frac{1}{|Ω|} \left. \frac{dE[ (I+ϵ) * L]}{dM}\right|_{ϵ=0}\]
where $ϵ$ is the strain. See O. Nielsen, R. Martin Phys. Rev. B. 32, 3792 (1985) for details. In Voigt notation one would use the vector $[σ_{xx} σ_{yy} σ_{zz} σ_{zy} σ_{zx} σ_{yx}]$.
sourceDFTK.compute_transfer_matrix — Methodcompute_transfer_matrix(
+ basis_in::PlaneWaveBasis,
kpt_in::Kpoint,
- basis_out::PlaneWaveBasis{T, VT} where VT<:Real,
+ basis_out::PlaneWaveBasis,
kpt_out::Kpoint
) -> Any
-
Return a sparse matrix that maps quantities given on basis_in and kpt_in to quantities on basis_out and kpt_out.
sourceDFTK.compute_transfer_matrix — Methodcompute_transfer_matrix(
- basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
- basis_out::PlaneWaveBasis{T, VT} where VT<:Real
-) -> Any
-
Return a list of sparse matrices (one per $k$-point) that map quantities given in the basis_in basis to quantities given in the basis_out basis.
sourceDFTK.compute_unit_cell_volume — Methodcompute_unit_cell_volume(lattice) -> Any
-
Compute unit cell volume volume. In case of 1D or 2D case, the volume is the length/surface.
sourceDFTK.compute_δHψ_sα — Methodcompute_δHψ_sα(
- basis::PlaneWaveBasis,
- ψ,
- q,
- s,
- α;
- kwargs...
-) -> Any
-
Assemble the right-hand side term for the Sternheimer equation for all relevant quantities: Compute the perturbation of the Hamiltonian with respect to a variation of the local potential produced by a displacement of the atom s in the direction α.
sourceDFTK.compute_δocc! — Methodcompute_δocc!(
+
Return a sparse matrix that maps quantities given on basis_in and kpt_in to quantities on basis_out and kpt_out.
sourceDFTK.compute_transfer_matrix — Methodcompute_transfer_matrix(
+ basis_in::PlaneWaveBasis,
+ basis_out::PlaneWaveBasis
+) -> Vector
+
Return a list of sparse matrices (one per $k$-point) that map quantities given in the basis_in basis to quantities given in the basis_out basis.
sourceDFTK.compute_unit_cell_volume — Methodcompute_unit_cell_volume(lattice) -> Any
+
Compute unit cell volume volume. In case of 1D or 2D case, the volume is the length/surface.
sourceDFTK.compute_δHψ_αs — Methodcompute_δHψ_αs(basis::PlaneWaveBasis, ψ, α, s, q) -> Any
+
Assemble the right-hand side term for the Sternheimer equation for all relevant quantities: Compute the perturbation of the Hamiltonian with respect to a variation of the local potential produced by a displacement of the atom s in the direction α.
sourceDFTK.compute_δocc! — Methodcompute_δocc!(
δocc,
basis::PlaneWaveBasis{T, VT} where VT<:Real,
ψ,
εF,
ε,
δHψ
-) -> NamedTuple{(:δocc, :δεF), _A} where _A<:Tuple{Any, Any}
-
Compute the derivatives of the occupations (and of the Fermi level). The derivatives of the occupations are in-place stored in δocc. The tuple (; δocc, δεF) is returned. It is assumed the passed δocc are initialised to zero.
sourceDFTK.compute_δψ! — Methodcompute_δψ!(
+) -> NamedTuple{(:δocc, :δεF), <:Tuple{Any, Any}}
+
Compute the derivatives of the occupations (and of the Fermi level). The derivatives of the occupations are in-place stored in δocc. The tuple (; δocc, δεF) is returned. It is assumed the passed δocc are initialised to zero.
sourceDFTK.compute_δψ! — Methodcompute_δψ!(
δψ,
basis::PlaneWaveBasis{T, VT} where VT<:Real,
H,
ψ,
εF,
ε,
- δHψ
+ δHψ;
+ ...
)
compute_δψ!(
δψ,
@@ -390,30 +376,30 @@
q,
kwargs_sternheimer...
)
-
Perform in-place computations of the derivatives of the wave functions by solving a Sternheimer equation for each k-points. It is assumed the passed δψ are initialised to zero.
sourceDFTK.compute_χ0 — Methodcompute_χ0(ham; temperature) -> Any
+
Perform in-place computations of the derivatives of the wave functions by solving a Sternheimer equation for each k-points. It is assumed the passed δψ are initialised to zero.
sourceDFTK.compute_χ0 — Methodcompute_χ0(ham; temperature) -> Any
Compute the independent-particle susceptibility. Will blow up for large systems. For non-spin-polarized calculations the matrix dimension is prod(basis.fft_size) × prod(basis.fft_size) and for collinear spin-polarized cases it is 2prod(basis.fft_size) × 2prod(basis.fft_size). In this case the matrix has effectively 4 blocks, which are:
\[\left(\begin{array}{cc}
(χ_0)_{αα} & (χ_0)_{αβ} \\
(χ_0)_{βα} & (χ_0)_{ββ}
-\end{array}\right)\]
sourceDFTK.cos2pi — Methodcos2pi(x) -> Any
-
Function to compute cos(2π x)
sourceDFTK.count_n_proj — Methodcount_n_proj(psps, psp_positions) -> Any
-
count_n_proj(psps, psp_positions)
Number of projector functions for all angular momenta up to psp.lmax and for all atoms in the system, including angular parts from -m:m.
sourceDFTK.count_n_proj — Methodcount_n_proj(psp::DFTK.NormConservingPsp, l::Integer) -> Any
-
count_n_proj(psp, l)
Number of projector functions for angular momentum l, including angular parts from -m:m.
sourceDFTK.count_n_proj — Methodcount_n_proj(psp::DFTK.NormConservingPsp) -> Int64
-
count_n_proj(psp)
Number of projector functions for all angular momenta up to psp.lmax, including angular parts from -m:m.
sourceDFTK.count_n_proj_radial — Methodcount_n_proj_radial(
+\end{array}\right)\]
sourceDFTK.cos2pi — Methodcos2pi(x) -> Any
+
Function to compute cos(2π x)
sourceDFTK.count_n_proj — Methodcount_n_proj(psps, psp_positions) -> Any
+
count_n_proj(psps, psp_positions)
Number of projector functions for all angular momenta up to psp.lmax and for all atoms in the system, including angular parts from -m:m.
sourceDFTK.count_n_proj — Methodcount_n_proj(psp::DFTK.NormConservingPsp, l::Integer) -> Any
+
count_n_proj(psp, l)
Number of projector functions for angular momentum l, including angular parts from -m:m.
sourceDFTK.count_n_proj — Methodcount_n_proj(psp::DFTK.NormConservingPsp) -> Int64
+
count_n_proj(psp)
Number of projector functions for all angular momenta up to psp.lmax, including angular parts from -m:m.
sourceDFTK.count_n_proj_radial — Methodcount_n_proj_radial(
psp::DFTK.NormConservingPsp,
l::Integer
) -> Any
-
count_n_proj_radial(psp, l)
Number of projector radial functions at angular momentum l.
sourceDFTK.count_n_proj_radial — Methodcount_n_proj_radial(psp::DFTK.NormConservingPsp) -> Int64
-
count_n_proj_radial(psp)
Number of projector radial functions at all angular momenta up to psp.lmax.
sourceDFTK.create_supercell — Methodcreate_supercell(
+
count_n_proj_radial(psp, l)
Number of projector radial functions at angular momentum l.
sourceDFTK.count_n_proj_radial — Methodcount_n_proj_radial(psp::DFTK.NormConservingPsp) -> Int64
+
count_n_proj_radial(psp)
Number of projector radial functions at all angular momenta up to psp.lmax.
sourceDFTK.create_supercell — Methodcreate_supercell(
lattice,
atoms,
positions,
supercell_size
-) -> NamedTuple{(:lattice, :atoms, :positions), _A} where _A<:Tuple{Any, Any, Any}
-
Construct a supercell of size supercell_size from a unit cell described by its lattice, atoms and their positions.
sourceDFTK.datadir_psp — Methoddatadir_psp() -> String
-
Return the data directory with pseudopotential files
sourceDFTK.default_fermialg — Methoddefault_fermialg(
+) -> NamedTuple{(:lattice, :atoms, :positions), <:Tuple{Any, Any, Any}}
+
Construct a supercell of size supercell_size from a unit cell described by its lattice, atoms and their positions.
sourceDFTK.datadir_psp — Methoddatadir_psp() -> String
+
Return the data directory with pseudopotential files
sourceDFTK.default_fermialg — Methoddefault_fermialg(
_::DFTK.Smearing.SmearingFunction
) -> FermiBisection
-
Default selection of a Fermi level determination algorithm
sourceDFTK.default_symmetries — Methoddefault_symmetries(
+
Default selection of a Fermi level determination algorithm
sourceDFTK.default_symmetries — Methoddefault_symmetries(
lattice,
atoms,
positions,
@@ -422,9 +408,9 @@
terms;
tol_symmetry
) -> Union{Vector{SymOp{Bool}}, Vector{SymOp{Float64}}}
-
Default logic to determine the symmetry operations to be used in the model.
sourceDFTK.default_wannier_centers — Methoddefault_wannier_centers(n_wannier) -> Any
-
Default random Gaussian guess for maximally-localised wannier functions generated in reduced coordinates.
sourceDFTK.determine_spin_polarization — Methoddetermine_spin_polarization(magnetic_moments) -> Symbol
-
:none if no element has a magnetic moment, else :collinear or :full.
sourceDFTK.diagonalize_all_kblocks — Methoddiagonalize_all_kblocks(
+
Default logic to determine the symmetry operations to be used in the model.
sourceDFTK.default_wannier_centers — Methoddefault_wannier_centers(n_wannier) -> Any
+
Default random Gaussian guess for maximally-localised wannier functions generated in reduced coordinates.
sourceDFTK.determine_spin_polarization — Methoddetermine_spin_polarization(magnetic_moments) -> Symbol
+
:none if no element has a magnetic moment, else :collinear or :full.
sourceDFTK.diagonalize_all_kblocks — Methoddiagonalize_all_kblocks(
eigensolver,
ham::Hamiltonian,
nev_per_kpoint::Int64;
@@ -435,29 +421,37 @@
miniter,
maxiter,
n_conv_check
-) -> NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), _A} where _A<:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}
-
Function for diagonalising each $k$-Point blow of ham one step at a time. Some logic for interpolating between $k$-points is used if interpolate_kpoints is true and if no guesses are given. eigensolver is the iterative eigensolver that really does the work, operating on a single $k$-Block. eigensolver should support the API eigensolver(A, X0; prec, tol, maxiter) prec_type should be a function that returns a preconditioner when called as prec(ham, kpt)
sourceDFTK.diameter — Methoddiameter(lattice::AbstractMatrix) -> Any
-
Compute the diameter of the unit cell
sourceDFTK.direct_minimization — Methoddirect_minimization(
- basis::PlaneWaveBasis;
+) -> NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), <:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}}
+
Function for diagonalising each $k$-Point blow of ham one step at a time. Some logic for interpolating between $k$-points is used if interpolate_kpoints is true and if no guesses are given. eigensolver is the iterative eigensolver that really does the work, operating on a single $k$-Block. eigensolver should support the API eigensolver(A, X0; prec, tol, maxiter) prec_type should be a function that returns a preconditioner when called as prec(ham, kpt)
sourceDFTK.diameter — Methoddiameter(lattice::AbstractMatrix) -> Any
+
Compute the diameter of the unit cell
sourceDFTK.direct_minimization — Methoddirect_minimization(
+ basis::PlaneWaveBasis{T, VT} where VT<:Real;
+ ψ,
+ tol,
+ is_converged,
+ maxiter,
+ prec_type,
+ callback,
+ optim_method,
+ linesearch,
kwargs...
-) -> NamedTuple{(:ham, :basis, :energies, :converged, :ρ, :ψ, :eigenvalues, :occupation, :εF, :optim_res), _A} where _A<:Tuple{Any, PlaneWaveBasis, Any, Bool, Any, Any, Vector{Any}, Vector, Nothing, Optim.MultivariateOptimizationResults{Optim.LBFGS{DFTK.DMPreconditioner, LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, typeof(DFTK.precondprep!)}, _A, _B, _C, _D, Bool} where {_A, _B, _C, _D}}
-
Computes the ground state by direct minimization. kwargs... are passed to Optim.Options(). Note that the resulting ψ are not necessarily eigenvectors of the Hamiltonian.
sourceDFTK.disable_threading — Methoddisable_threading() -> Union{Nothing, Bool}
-
Convenience function to disable all threading in DFTK and assert that Julia threading is off as well.
sourceDFTK.divergence_real — Methoddivergence_real(operand, basis) -> Any
-
Compute divergence of an operand function, which returns the cartesian x,y,z components in real space when called with the arguments 1 to 3. The divergence is also returned as a real-space array.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
+) -> Any
+
Computes the ground state by direct minimization. kwargs... are passed to Optim.Options() and optim_method selects the optim approach which is employed.
sourceDFTK.disable_threading — Methoddisable_threading() -> Union{Nothing, Bool}
+
Convenience function to disable all threading in DFTK and assert that Julia threading is off as well.
sourceDFTK.divergence_real — Methoddivergence_real(operand, basis) -> Any
+
Compute divergence of an operand function, which returns the cartesian x,y,z components in real space when called with the arguments 1 to 3. The divergence is also returned as a real-space array.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
lattice::AbstractArray{T},
charges::AbstractArray,
positions;
kwargs...
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Standard computation of energy and forces.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Standard computation of energy and forces.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
lattice::AbstractArray{T},
charges,
positions,
q,
ph_disp;
kwargs...
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Computation for phonons; required to build the dynamical matrix.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Computation for phonons; required to build the dynamical matrix.
sourceDFTK.energy_forces_ewald — Methodenergy_forces_ewald(
S,
lattice::AbstractArray{T},
charges,
@@ -465,16 +459,16 @@
q,
ph_disp;
η
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Compute the electrostatic energy and forces. The energy is the electrostatic interaction energy per unit cell between point charges in a uniform background of compensating charge to yield net neutrality. The forces is the opposite of the derivative of the energy with respect to positions.
lattice should contain the lattice vectors as columns. charges and positions are the point charges and their positions (as an array of arrays) in fractional coordinates.
For now this function returns zero energy and force on non-3D systems. Use a pairwise potential term if you want to customise this treatment.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Compute the electrostatic energy and forces. The energy is the electrostatic interaction energy per unit cell between point charges in a uniform background of compensating charge to yield net neutrality. The forces is the opposite of the derivative of the energy with respect to positions.
lattice should contain the lattice vectors as columns. charges and positions are the point charges and their positions (as an array of arrays) in fractional coordinates.
For now this function returns zero energy and force on non-3D systems. Use a pairwise potential term if you want to customise this treatment.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
lattice::AbstractArray{T},
symbols,
positions,
V,
params;
kwargs...
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Standard computation of energy and forces.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Standard computation of energy and forces.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
lattice::AbstractArray{T},
symbols,
positions,
@@ -483,8 +477,8 @@
q,
ph_disp;
kwargs...
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Computation for phonons; required to build the dynamical matrix.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Computation for phonons; required to build the dynamical matrix.
sourceDFTK.energy_forces_pairwise — Methodenergy_forces_pairwise(
S,
lattice::AbstractArray{T},
symbols,
@@ -494,90 +488,100 @@
q,
ph_disp;
max_radius
-) -> NamedTuple{(:energy, :forces), _A} where _A<:Tuple{Any, Any}
-
Compute the pairwise energy and forces. The energy is the interaction energy per unit cell between atomic sites. The forces is the opposite of the derivative of the energy with respect to positions.
lattice should contain the lattice vectors as columns. symbols and positions are the atomic elements and their positions (as an array of arrays) in fractional coordinates. V and params are the pairwise potential and its set of parameters (that depends on pairs of symbols).
The potential is expected to decrease quickly at infinity.
sourceDFTK.energy_psp_correction — Methodenergy_psp_correction(
+) -> NamedTuple{(:energy, :forces), <:Tuple{Any, Any}}
+
Compute the pairwise energy and forces. The energy is the interaction energy per unit cell between atomic sites. The forces is the opposite of the derivative of the energy with respect to positions.
lattice should contain the lattice vectors as columns. symbols and positions are the atomic elements and their positions (as an array of arrays) in fractional coordinates. V and params are the pairwise potential and its set of parameters (that depends on pairs of symbols).
The potential is expected to decrease quickly at infinity.
sourceDFTK.energy_psp_correction — Methodenergy_psp_correction(
lattice::AbstractArray{T, 2},
atoms,
atom_groups
) -> Any
-
Compute the correction term for properly modelling the interaction of the pseudopotential core with the compensating background charge induced by the Ewald term.
sourceDFTK.enforce_real! — Methodenforce_real!(
+
Compute the correction term for properly modelling the interaction of the pseudopotential core with the compensating background charge induced by the Ewald term.
sourceDFTK.enforce_real! — Methodenforce_real!(
fourier_coeffs,
basis::PlaneWaveBasis
) -> AbstractArray
-
Ensure its real-space equivalent of passed Fourier-space representation is entirely real by removing wavevectors G that don't have a -G counterpart in the basis.
sourceDFTK.estimate_integer_lattice_bounds — Methodestimate_integer_lattice_bounds(
+
Ensure its real-space equivalent of passed Fourier-space representation is entirely real by removing wavevectors G that don't have a -G counterpart in the basis.
sourceDFTK.estimate_integer_lattice_bounds — Methodestimate_integer_lattice_bounds(
M::AbstractArray{T, 2},
- δ
-) -> Any
+ δ;
+ ...
+) -> Vector
estimate_integer_lattice_bounds(
M::AbstractArray{T, 2},
δ,
shift;
tol
-) -> Any
-
Estimate integer bounds for dense space loops from a given inequality ||Mx|| ≤ δ. For 1D and 2D systems the limit will be zero in the auxiliary dimensions.
sourceDFTK.eval_psp_density_core_fourier — Methodeval_psp_density_core_fourier(
+) -> Vector
+
Estimate integer bounds for dense space loops from a given inequality ||Mx|| ≤ δ. For 1D and 2D systems the limit will be zero in the auxiliary dimensions.
sourceDFTK.eval_psp_density_core_fourier — Methodeval_psp_density_core_fourier(
_::DFTK.NormConservingPsp,
_::Real
-) -> Real
-
eval_psp_density_core_fourier(psp, q)
Evaluate the atomic core charge density in reciprocal space: ρval(q) = ∫{R^3} ρcore(r) e^{-iqr} dr = 4π ∫{R+} ρcore(r) sin(qr)/qr r^2 dr
sourceDFTK.eval_psp_density_core_real — Methodeval_psp_density_core_real(
+) -> Any
+
eval_psp_density_core_fourier(psp, p)
Evaluate the atomic core charge density in reciprocal space:
\[\begin{aligned}
+ρ_{\rm core}(p) &= ∫_{ℝ^3} ρ_{\rm core}(r) e^{-ip·r} dr \\
+ &= 4π ∫_{ℝ_+} ρ_{\rm core}(r) \frac{\sin(p·r)}{ρ·r} r^2 dr.
+\end{aligned}\]
sourceDFTK.eval_psp_density_core_real — Methodeval_psp_density_core_real(
_::DFTK.NormConservingPsp,
_::Real
) -> Any
-
eval_psp_density_core_real(psp, r)
Evaluate the atomic core charge density in real space.
sourceDFTK.eval_psp_density_valence_fourier — Methodeval_psp_density_valence_fourier(
+
eval_psp_density_core_real(psp, r)
Evaluate the atomic core charge density in real space.
sourceDFTK.eval_psp_density_valence_fourier — Methodeval_psp_density_valence_fourier(
psp::DFTK.NormConservingPsp,
- q::AbstractVector
-) -> Real
-
eval_psp_density_valence_fourier(psp, q)
Evaluate the atomic valence charge density in reciprocal space: ρval(q) = ∫{R^3} ρval(r) e^{-iqr} dr = 4π ∫{R+} ρval(r) sin(qr)/qr r^2 dr
sourceDFTK.eval_psp_density_valence_real — Methodeval_psp_density_valence_real(
+ p::AbstractVector
+) -> Any
+
eval_psp_density_valence_fourier(psp, p)
Evaluate the atomic valence charge density in reciprocal space:
\[\begin{aligned}
+ρ_{\rm val}(p) &= ∫_{ℝ^3} ρ_{\rm val}(r) e^{-ip·r} dr \\
+ &= 4π ∫_{ℝ_+} ρ_{\rm val}(r) \frac{\sin(p·r)}{ρ·r} r^2 dr.
+\end{aligned}\]
sourceDFTK.eval_psp_density_valence_real — Methodeval_psp_density_valence_real(
psp::DFTK.NormConservingPsp,
r::AbstractVector
) -> Any
-
eval_psp_density_valence_real(psp, r)
Evaluate the atomic valence charge density in real space.
sourceDFTK.eval_psp_energy_correction — Functioneval_psp_energy_correction([T=Float64,] psp, n_electrons)
Evaluate the energy correction to the Ewald electrostatic interaction energy of one unit cell, which is required compared the Ewald expression for point-like nuclei. n_electrons is the number of electrons per unit cell. This defines the uniform compensating background charge, which is assumed here.
Notice: The returned result is the energy per unit cell and not the energy per volume. To obtain the latter, the caller needs to divide by the unit cell volume.
The energy correction is defined as the limit of the Fourier-transform of the local potential as $q \to 0$, using the same correction as in the Fourier-transform of the local potential: math \lim_{q \to 0} 4π N_{\rm elec} ∫_{ℝ_+} (V(r) - C(r)) \frac{\sin(qr)}{qr} r^2 dr + F[C(r)] = 4π N_{\rm elec} ∫_{ℝ_+} (V(r) + Z/r) r^2 dr
sourceDFTK.eval_psp_local_fourier — Methodeval_psp_local_fourier(
+
eval_psp_density_valence_real(psp, r)
Evaluate the atomic valence charge density in real space.
sourceDFTK.eval_psp_energy_correction — Functioneval_psp_energy_correction([T=Float64,] psp, n_electrons)
Evaluate the energy correction to the Ewald electrostatic interaction energy of one unit cell, which is required compared the Ewald expression for point-like nuclei. n_electrons is the number of electrons per unit cell. This defines the uniform compensating background charge, which is assumed here.
Notice: The returned result is the energy per unit cell and not the energy per volume. To obtain the latter, the caller needs to divide by the unit cell volume.
The energy correction is defined as the limit of the Fourier-transform of the local potential as $p \to 0$, using the same correction as in the Fourier-transform of the local potential:
\[\lim_{p \to 0} 4π N_{\rm elec} ∫_{ℝ_+} (V(r) - C(r)) \frac{\sin(p·r)}{p·r} r^2 dr + F[C(r)]
+ = 4π N_{\rm elec} ∫_{ℝ_+} (V(r) + Z/r) r^2 dr.\]
sourceDFTK.eval_psp_local_fourier — Methodeval_psp_local_fourier(
psp::DFTK.NormConservingPsp,
- q::AbstractVector
+ p::AbstractVector
) -> Any
-
eval_psp_local_fourier(psp, q)
Evaluate the local part of the pseudopotential in reciprocal space:
\[\begin{aligned}
-V_{\rm loc}(q) &= ∫_{ℝ^3} V_{\rm loc}(r) e^{-iqr} dr \\
- &= 4π ∫_{ℝ_+} V_{\rm loc}(r) \frac{\sin(qr)}{q} r dr
+
eval_psp_local_fourier(psp, p)
Evaluate the local part of the pseudopotential in reciprocal space:
\[\begin{aligned}
+V_{\rm loc}(p) &= ∫_{ℝ^3} V_{\rm loc}(r) e^{-ip·r} dr \\
+ &= 4π ∫_{ℝ_+} V_{\rm loc}(r) \frac{\sin(p·r)}{p} r dr
\end{aligned}\]
In practice, the local potential should be corrected using a Coulomb-like term $C(r) = -Z/r$ to remove the long-range tail of $V_{\rm loc}(r)$ from the integral:
\[\begin{aligned}
-V_{\rm loc}(q) &= ∫_{ℝ^3} (V_{\rm loc}(r) - C(r)) e^{-iq·r} dr + F[C(r)] \\
- &= 4π ∫_{ℝ_+} (V_{\rm loc}(r) + Z/r) \frac{\sin(qr)}{qr} r^2 dr - Z/q^2
-\end{aligned}\]
sourceDFTK.eval_psp_local_real — Methodeval_psp_local_real(
+V_{\rm loc}(p) &= ∫_{ℝ^3} (V_{\rm loc}(r) - C(r)) e^{-ip·r} dr + F[C(r)] \\
+ &= 4π ∫_{ℝ_+} (V_{\rm loc}(r) + Z/r) \frac{\sin(p·r)}{p·r} r^2 dr - Z/p^2.
+\end{aligned}\]
sourceDFTK.eval_psp_local_real — Methodeval_psp_local_real(
psp::DFTK.NormConservingPsp,
r::AbstractVector
) -> Any
-
eval_psp_local_real(psp, r)
Evaluate the local part of the pseudopotential in real space.
sourceDFTK.eval_psp_projector_fourier — Methodeval_psp_projector_fourier(
+
eval_psp_local_real(psp, r)
Evaluate the local part of the pseudopotential in real space.
sourceDFTK.eval_psp_projector_fourier — Methodeval_psp_projector_fourier(
psp::DFTK.NormConservingPsp,
- q::AbstractVector
+ p::AbstractVector
)
-
eval_psp_projector_fourier(psp, i, l, q)
Evaluate the radial part of the i-th projector for angular momentum l at the reciprocal vector with modulus q:
\[\begin{aligned}
-p(q) &= ∫_{ℝ^3} p_{il}(r) e^{-iq·r} dr \\
- &= 4π ∫_{ℝ_+} r^2 p_{il}(r) j_l(qr) dr
-\end{aligned}\]
sourceDFTK.eval_psp_projector_real — Methodeval_psp_projector_real(
+
eval_psp_projector_fourier(psp, i, l, p)
Evaluate the radial part of the i-th projector for angular momentum l at the reciprocal vector with modulus p:
\[\begin{aligned}
+{\rm proj}(p) &= ∫_{ℝ^3} {\rm proj}_{il}(r) e^{-ip·r} dr \\
+ &= 4π ∫_{ℝ_+} r^2 {\rm proj}_{il}(r) j_l(p·r) dr.
+\end{aligned}\]
sourceDFTK.eval_psp_projector_real — Methodeval_psp_projector_real(
psp::DFTK.NormConservingPsp,
i,
l,
r::AbstractVector
) -> Any
-
eval_psp_projector_real(psp, i, l, r)
Evaluate the radial part of the i-th projector for angular momentum l in real-space at the vector with modulus r.
sourceDFTK.filled_occupation — Methodfilled_occupation(model) -> Int64
-
Maximal occupation of a state (2 for non-spin-polarized electrons, 1 otherwise).
sourceDFTK.find_equivalent_kpt — Methodfind_equivalent_kpt(
+
eval_psp_projector_real(psp, i, l, r)
Evaluate the radial part of the i-th projector for angular momentum l in real-space at the vector with modulus r.
sourceDFTK.filled_occupation — Methodfilled_occupation(model) -> Int64
+
Maximal occupation of a state (2 for non-spin-polarized electrons, 1 otherwise).
sourceDFTK.find_equivalent_kpt — Methodfind_equivalent_kpt(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
kcoord,
spin;
tol
-) -> NamedTuple{(:index, :ΔG), _A} where _A<:Tuple{Int64, Any}
-
Find the equivalent index of the coordinate kcoord ∈ ℝ³ in a list kcoords ∈ [-½, ½)³. ΔG is the vector of ℤ³ such that kcoords[index] = kcoord + ΔG.
sourceDFTK.gather_kpts — Methodgather_kpts(
- data::AbstractArray,
- basis::PlaneWaveBasis
-) -> Any
-
Gather the distributed data of a quantity depending on k-Points on the master process and return it. On the other (non-master) processes nothing is returned.
sourceDFTK.gather_kpts — Methodgather_kpts(
+) -> NamedTuple{(:index, :ΔG), <:Tuple{Int64, Any}}
+
Find the equivalent index of the coordinate kcoord ∈ ℝ³ in a list kcoords ∈ [-½, ½)³. ΔG is the vector of ℤ³ such that kcoords[index] = kcoord + ΔG.
sourceDFTK.gather_kpts — Methodgather_kpts(
basis::PlaneWaveBasis
) -> Union{Nothing, PlaneWaveBasis}
-
Gather the distributed $k$-point data on the master process and return it as a PlaneWaveBasis. On the other (non-master) processes nothing is returned. The returned object should not be used for computations and only to extract data for post-processing and serialisation to disk.
sourceDFTK.gaussian_valence_charge_density_fourier — Methodgaussian_valence_charge_density_fourier(
+
Gather the distributed $k$-point data on the master process and return it as a PlaneWaveBasis. On the other (non-master) processes nothing is returned. The returned object should not be used for computations and only for debugging or to extract data for serialisation to disk.
sourceDFTK.gather_kpts_block! — Methodgather_kpts_block!(
+ dest,
+ basis::PlaneWaveBasis,
+ kdata::AbstractArray{A, 1}
+) -> Any
+
Gather the distributed data of a quantity depending on k-Points on the master process and save it in dest as a dense (size(kdata[1])..., n_kpoints) array. On the other (non-master) processes nothing is returned.
sourceDFTK.gaussian_valence_charge_density_fourier — Methodgaussian_valence_charge_density_fourier(
el::DFTK.Element,
- q::Real
-) -> Real
-
Gaussian valence charge density using Abinit's coefficient table, in Fourier space.
sourceDFTK.guess_density — Functionguess_density(
+ p::Real
+) -> Any
+
Gaussian valence charge density using Abinit's coefficient table, in Fourier space.
sourceDFTK.guess_density — Functionguess_density(
basis::PlaneWaveBasis,
- method::AtomicDensity
+ method::AtomicDensity;
+ ...
) -> Any
guess_density(
basis::PlaneWaveBasis,
@@ -586,74 +590,102 @@
n_electrons
) -> Any
guess_density(basis::PlaneWaveBasis, method::DensityConstructionMethod,
- magnetic_moments=[]; n_electrons=basis.model.n_electrons)
Build a superposition of atomic densities (SAD) guess density or a rarndom guess density.
The guess atomic densities are taken as one of the following depending on the input method:
-RandomDensity(): A random density, normalized to the number of electrons basis.model.n_electrons. Does not support magnetic moments. -ValenceDensityAuto(): A combination of the ValenceDensityGaussian and ValenceDensityPseudo methods where elements whose pseudopotentials provide numeric valence charge density data use them and elements without use Gaussians. -ValenceDensityGaussian(): Gaussians of length specified by atom_decay_length normalized for the correct number of electrons:
\[\hat{ρ}(G) = Z_{\mathrm{valence}} \exp\left(-(2π \text{length} |G|)^2\right)\]
ValenceDensityPseudo(): Numerical pseudo-atomic valence charge densities from the
pseudopotentials. Will fail if one or more elements in the system has a pseudopotential that does not have valence charge density data.
When magnetic moments are provided, construct a symmetry-broken density guess. The magnetic moments should be specified in units of $μ_B$.
sourceDFTK.hamiltonian_with_total_potential — Methodhamiltonian_with_total_potential(
+ magnetic_moments=[]; n_electrons=basis.model.n_electrons)
Build a superposition of atomic densities (SAD) guess density or a rarndom guess density.
The guess atomic densities are taken as one of the following depending on the input method:
-RandomDensity(): A random density, normalized to the number of electrons basis.model.n_electrons. Does not support magnetic moments. -ValenceDensityAuto(): A combination of the ValenceDensityGaussian and ValenceDensityPseudo methods where elements whose pseudopotentials provide numeric valence charge density data use them and elements without use Gaussians. -ValenceDensityGaussian(): Gaussians of length specified by atom_decay_length normalized for the correct number of electrons:
\[\hat{ρ}(G) = Z_{\mathrm{valence}} \exp\left(-(2π \text{length} |G|)^2\right)\]
ValenceDensityPseudo(): Numerical pseudo-atomic valence charge densities from the
pseudopotentials. Will fail if one or more elements in the system has a pseudopotential that does not have valence charge density data.
When magnetic moments are provided, construct a symmetry-broken density guess. The magnetic moments should be specified in units of $μ_B$.
sourceDFTK.hamiltonian_with_total_potential — Methodhamiltonian_with_total_potential(
ham::Hamiltonian,
V
) -> Hamiltonian
-
Returns a new Hamiltonian with local potential replaced by the given one
sourceDFTK.hankel — Methodhankel(
+
Returns a new Hamiltonian with local potential replaced by the given one
sourceDFTK.hankel — Methodhankel(
r::AbstractVector,
r2_f::AbstractVector,
l::Integer,
- q::Real
-) -> Real
-
hankel(r, r2_f, l, q)
Compute the Hankel transform
\[ H[f] = 4\pi \int_0^\infty r f(r) j_l(qr) r dr.\]
The integration is performed by trapezoidal quadrature, and the function takes as input the radial grid r, the precomputed quantity r²f(r) r2_f, angular momentum / spherical bessel order l, and the Hankel coordinate q.
sourceDFTK.has_core_density — Methodhas_core_density(_::DFTK.Element) -> Any
-
Check presence of model core charge density (non-linear core correction).
sourceDFTK.index_G_vectors — Methodindex_G_vectors(
+ p::Real
+) -> Any
+
hankel(r, r2_f, l, p)
Compute the Hankel transform
\[ H[f] = 4\pi \int_0^\infty r f(r) j_l(p·r) r dr.\]
The integration is performed by trapezoidal quadrature, and the function takes as input the radial grid r, the precomputed quantity r²f(r) r2_f, angular momentum / spherical bessel order l, and the Hankel coordinate p.
sourceDFTK.has_core_density — Methodhas_core_density(_::DFTK.Element) -> Any
+
Check presence of model core charge density (non-linear core correction).
sourceDFTK.index_G_vectors — Methodindex_G_vectors(
fft_size::Tuple,
G::AbstractVector{<:Integer}
) -> Any
-
Return the index tuple I such that G_vectors(basis)[I] == G or the index i such that G_vectors(basis, kpoint)[i] == G. Returns nothing if outside the range of valid wave vectors.
sourceDFTK.interpolate_density — Methodinterpolate_density(
- ρ_in,
+
Return the index tuple I such that G_vectors(basis)[I] == G or the index i such that G_vectors(basis, kpoint)[i] == G. Returns nothing if outside the range of valid wave vectors.
sourceDFTK.interpolate_density — Methodinterpolate_density(
+ ρ_in::AbstractArray{T, 4},
basis_in::PlaneWaveBasis,
basis_out::PlaneWaveBasis
-) -> Any
-
Interpolate a function expressed in a basis basis_in to a basis basis_out. This interpolation uses a very basic real-space algorithm, and makes a DWIM-y attempt to take into account the fact that basis_out can be a supercell of basis_in.
sourceDFTK.interpolate_kpoint — Methodinterpolate_kpoint(
+) -> AbstractArray{T, 4} where T
+
Interpolate a density expressed in a basis basis_in to a basis basis_out. This interpolation uses a very basic real-space algorithm, and makes a DWIM-y attempt to take into account the fact that basis_out can be a supercell of basis_in.
sourceDFTK.interpolate_density — Methodinterpolate_density(
+ ρ_in::AbstractArray{T, 4},
+ grid_in::Tuple{T, T, T} where T,
+ grid_out::Tuple{T, T, T} where T,
+ lattice_in,
+ lattice_out
+) -> AbstractArray{T, 4} where T
+
Interpolate a density in real space from one FFT grid to another, where lattice_in and lattice_out may be supercells of each other.
sourceDFTK.interpolate_density — Methodinterpolate_density(
+ ρ_in::AbstractArray{T, 4},
+ grid_out::Tuple{T, T, T} where T
+) -> AbstractArray{T, 4} where T
+
Interpolate a density in real space from one FFT grid to another. Assumes the lattice is unchanged.
sourceDFTK.interpolate_kpoint — Methodinterpolate_kpoint(
data_in::AbstractVecOrMat,
basis_in::PlaneWaveBasis,
kpoint_in::Kpoint,
basis_out::PlaneWaveBasis,
kpoint_out::Kpoint
) -> Any
-
Interpolate some data from one $k$-point to another. The interpolation is fast, but not necessarily exact. Intended only to construct guesses for iterative solvers.
sourceDFTK.irfft — Methodirfft(
+
Interpolate some data from one $k$-point to another. The interpolation is fast, but not necessarily exact. Intended only to construct guesses for iterative solvers.
sourceDFTK.irfft — Methodirfft(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
f_fourier::AbstractArray
) -> Any
-
Perform a real valued iFFT; see ifft. Note that this function silently drops the imaginary part.
sourceDFTK.irreducible_kcoords — Methodirreducible_kcoords(
+
Perform a real valued iFFT; see ifft. Note that this function silently drops the imaginary part.
sourceDFTK.irreducible_kcoords — Methodirreducible_kcoords(
kgrid::MonkhorstPack,
symmetries::AbstractVector{<:SymOp};
check_symmetry
-) -> Union{NamedTuple{(:kcoords, :kweights), Tuple{Vector{StaticArraysCore.SVector{3, Rational{Int64}}}, Vector{Float64}}}, NamedTuple{(:kcoords, :kweights), Tuple{Vector{StaticArraysCore.SVector{3, Float64}}, Vector{Float64}}}}
-
Construct the irreducible wedge given the crystal symmetries. Returns the list of k-point coordinates and the associated weights.
sourceDFTK.is_metal — Methodis_metal(eigenvalues, εF; tol) -> Bool
-
is_metal(eigenvalues, εF; tol)
Determine whether the provided bands indicate the material is a metal, i.e. where bands are cut by the Fermi level.
sourceDFTK.k_to_equivalent_kpq_permutation — Methodk_to_equivalent_kpq_permutation(
+) -> Union{@NamedTuple{kcoords::Vector{StaticArraysCore.SVector{3, Rational{Int64}}}, kweights::Vector{Float64}}, @NamedTuple{kcoords::Vector{StaticArraysCore.SVector{3, Float64}}, kweights::Vector{Float64}}}
+
Construct the irreducible wedge given the crystal symmetries. Returns the list of k-point coordinates and the associated weights.
sourceDFTK.is_metal — Methodis_metal(eigenvalues, εF; tol) -> Bool
+
is_metal(eigenvalues, εF; tol)
Determine whether the provided bands indicate the material is a metal, i.e. where bands are cut by the Fermi level.
sourceDFTK.k_to_equivalent_kpq_permutation — Methodk_to_equivalent_kpq_permutation(
basis::PlaneWaveBasis,
qcoord
-) -> Any
-
Return the indices of the kpoints shifted by q. That is for each kpoint of the basis: kpoints[ik].coordinate + q is equivalent to kpoints[indices[ik]].coordinate.
sourceDFTK.kgrid_from_maximal_spacing — Methodkgrid_from_maximal_spacing(
+) -> Vector
+
Return the indices of the kpoints shifted by q. That is for each kpoint of the basis: kpoints[ik].coordinate + q is equivalent to kpoints[indices[ik]].coordinate.
sourceDFTK.kgrid_from_maximal_spacing — Methodkgrid_from_maximal_spacing(
lattice,
spacing;
kshift
) -> Union{MonkhorstPack, Vector{Int64}}
-
Build a MonkhorstPack grid to ensure kpoints are at most this spacing apart (in inverse Bohrs). A reasonable spacing is 0.13 inverse Bohrs (around $2π * 0.04 \AA^{-1}$).
sourceDFTK.kgrid_from_minimal_n_kpoints — Methodkgrid_from_minimal_n_kpoints(
+
Build a MonkhorstPack grid to ensure kpoints are at most this spacing apart (in inverse Bohrs). A reasonable spacing is 0.13 inverse Bohrs (around $2π * 0.04 \AA^{-1}$).
sourceDFTK.kgrid_from_minimal_n_kpoints — Methodkgrid_from_minimal_n_kpoints(
lattice,
n_kpoints::Integer;
kshift
) -> Union{MonkhorstPack, Vector{Int64}}
-
Selects a MonkhorstPack grid size which ensures that at least a n_kpoints total number of $k$-points are used. The distribution of $k$-points amongst coordinate directions is as uniformly as possible, trying to achieve an identical minimal spacing in all directions.
sourceDFTK.kpath_get_kcoords — Methodkpath_get_kcoords(
+
Selects a MonkhorstPack grid size which ensures that at least a n_kpoints total number of $k$-points are used. The distribution of $k$-points amongst coordinate directions is as uniformly as possible, trying to achieve an identical minimal spacing in all directions.
sourceDFTK.kpath_get_kcoords — Methodkpath_get_kcoords(
kinter::Brillouin.KPaths.KPathInterpolant{D}
-) -> Any
-
Return kpoint coordinates in reduced coordinates
sourceDFTK.kpq_equivalent_blochwave_to_kpq — Methodkpq_equivalent_blochwave_to_kpq(
+) -> Vector
+
Return kpoint coordinates in reduced coordinates
sourceDFTK.kpq_equivalent_blochwave_to_kpq — Methodkpq_equivalent_blochwave_to_kpq(
basis,
kpt,
q,
ψk_plus_q_equivalent
-) -> NamedTuple{(:kpt, :ψk), _A} where _A<:Tuple{Kpoint, Any}
-
Create the Fourier expansion of $ψ_{k+q}$ from $ψ_{[k+q]}$, where $[k+q]$ is in basis.kpoints. while $k+q$ may or may not be inside.
If $ΔG ≔ [k+q] - (k+q)$, then we have that
\[ ∑_G \hat{u}_{[k+q]}(G) e^{i(k+q+G)·r} &= ∑_{G'} \hat{u}_{k+q}(G'-ΔG) e^{i(k+q+ΔG+G')·r},\]
hence
\[ u_{k+q}(G) = u_{[k+q]}(G + ΔG).\]
sourceDFTK.krange_spin — Methodkrange_spin(basis::PlaneWaveBasis, spin::Integer) -> Any
-
Return the index range of $k$-points that have a particular spin component.
sourceDFTK.list_psp — Functionlist_psp() -> Any
+) -> NamedTuple{(:kpt, :ψk), <:Tuple{Kpoint, Any}}
+
Create the Fourier expansion of $ψ_{k+q}$ from $ψ_{[k+q]}$, where $[k+q]$ is in basis.kpoints. while $k+q$ may or may not be inside.
If $ΔG ≔ [k+q] - (k+q)$, then we have that
\[ ∑_G \hat{u}_{[k+q]}(G) e^{i(k+q+G)·r} &= ∑_{G'} \hat{u}_{k+q}(G'-ΔG) e^{i(k+q+ΔG+G')·r},\]
hence
\[ u_{k+q}(G) = u_{[k+q]}(G + ΔG).\]
sourceDFTK.krange_spin — Methodkrange_spin(basis::PlaneWaveBasis, spin::Integer) -> Any
+
Return the index range of $k$-points that have a particular spin component.
sourceDFTK.kwargs_scf_checkpoints — Methodkwargs_scf_checkpoints(
+ basis::DFTK.AbstractBasis;
+ filename,
+ callback,
+ diagtolalg,
+ ρ,
+ ψ,
+ save_ψ,
+ kwargs...
+) -> NamedTuple{(:callback, :diagtolalg, :ψ, :ρ), <:Tuple{ComposedFunction{ScfDefaultCallback, ScfSaveCheckpoints}, AdaptiveDiagtol, Any, Any}}
+
Transparently handle checkpointing by either returning kwargs for self_consistent_field, which start checkpointing (if no checkpoint file is present) or that continue a checkpointed run (if a checkpoint file can be loaded). filename is the location where the checkpoint is saved, save_ψ determines whether orbitals are saved in the checkpoint as well. The latter is discouraged, since generally slow.
sourceDFTK.list_psp — Functionlist_psp(; ...) -> Any
list_psp(element; family, functional, core) -> Any
-
list_psp(element; functional, family, core)
List the pseudopotential files known to DFTK. Allows various ways to restrict the displayed files.
Examples
julia> list_psp(; family="hgh")
will list all HGH-type pseudopotentials and
julia> list_psp(; family="hgh", functional="lda")
will only list those for LDA (also known as Pade in this context) and
julia> list_psp(:O, core=:semicore)
will list all oxygen semicore pseudopotentials known to DFTK.
sourceDFTK.load_psp — Methodload_psp(
+
list_psp(element; functional, family, core)
List the pseudopotential files known to DFTK. Allows various ways to restrict the displayed files.
Examples
julia> list_psp(; family="hgh")
will list all HGH-type pseudopotentials and
julia> list_psp(; family="hgh", functional="lda")
will only list those for LDA (also known as Pade in this context) and
julia> list_psp(:O, core=:semicore)
will list all oxygen semicore pseudopotentials known to DFTK.
sourceDFTK.load_psp — Methodload_psp(
key::AbstractString;
kwargs...
-) -> Union{PspHgh{Float64}, PspUpf}
-
Load a pseudopotential file from the library of pseudopotentials. The file is searched in the directory datadir_psp() and by the key. If the key is a path to a valid file, the extension is used to determine the type of the pseudopotential file format and a respective class is returned.
sourceDFTK.load_scfres — Functionload_scfres(filename)
Load back an scfres, which has previously been stored with save_scfres. Note the warning in save_scfres.
sourceDFTK.model_DFT — Methodmodel_DFT(
+) -> Union{PspHgh{Float64}, PspUpf{_A, Interpolations.Extrapolation{T, 1, ITPT, IT, Interpolations.Throw{Nothing}}} where {_A, T, ITPT, IT}}
+
Load a pseudopotential file from the library of pseudopotentials. The file is searched in the directory datadir_psp() and by the key. If the key is a path to a valid file, the extension is used to determine the type of the pseudopotential file format and a respective class is returned.
sourceDFTK.load_scfres — Functionload_scfres(filename::AbstractString; ...) -> Any
+load_scfres(
+ filename::AbstractString,
+ basis;
+ skip_hamiltonian,
+ strict
+) -> Any
+
Load back an scfres, which has previously been stored with save_scfres. Note the warning in save_scfres.
If basis is nothing, the basis is also loaded and reconstructed from the file, in which case architecture=CPU(). If a basis is passed, this one is used, which can be used to continue computation on a slightly different model or to avoid the cost of rebuilding the basis. If the stored basis and the passed basis are inconsistent (e.g. different FFT size, Ecut, k-points etc.) the load_scfres will error out.
By default the energies and ham (Hamiltonian object) are recomputed. To avoid this, set skip_hamiltonian=true. On errors the routine exits unless strict=false in which case it tries to recover from the file as much data as it can, but then the resulting scfres might not be fully consistent.
No compatibility guarantees No guarantees are made with respect to this function at this point. It may change incompatibly between DFTK versions (including patch versions) or stop working / be removed in the future.
sourceDFTK.model_DFT — Methodmodel_DFT(
lattice::AbstractMatrix,
atoms::Vector{<:DFTK.Element},
positions::Vector{<:AbstractVector},
@@ -661,25 +693,25 @@
extra_terms,
kwargs...
) -> Model
-
Build a DFT model from the specified atoms, with the specified functionals.
sourceDFTK.model_LDA — Methodmodel_LDA(
+
Build a DFT model from the specified atoms, with the specified functionals.
sourceDFTK.model_LDA — Methodmodel_LDA(
lattice::AbstractMatrix,
atoms::Vector{<:DFTK.Element},
positions::Vector{<:AbstractVector};
kwargs...
) -> Model
-
Build an LDA model (Perdew & Wang parametrization) from the specified atoms. DOI:10.1103/PhysRevB.45.13244
sourceDFTK.model_PBE — Methodmodel_PBE(
+
Build an LDA model (Perdew & Wang parametrization) from the specified atoms. https://doi.org/10.1103/PhysRevB.45.13244
sourceDFTK.model_PBE — Methodmodel_PBE(
lattice::AbstractMatrix,
atoms::Vector{<:DFTK.Element},
positions::Vector{<:AbstractVector};
kwargs...
) -> Model
-
Build an PBE-GGA model from the specified atoms. DOI:10.1103/PhysRevLett.77.3865
sourceDFTK.model_SCAN — Methodmodel_SCAN(
+
Build an PBE-GGA model from the specified atoms. https://doi.org/10.1103/PhysRevLett.77.3865
sourceDFTK.model_SCAN — Methodmodel_SCAN(
lattice::AbstractMatrix,
atoms::Vector{<:DFTK.Element},
positions::Vector{<:AbstractVector};
kwargs...
) -> Model
-
Build a SCAN meta-GGA model from the specified atoms. DOI:10.1103/PhysRevLett.115.036402
sourceDFTK.model_atomic — Methodmodel_atomic(
+
Build a SCAN meta-GGA model from the specified atoms. https://doi.org/10.1103/PhysRevLett.115.036402
sourceDFTK.model_atomic — Methodmodel_atomic(
lattice::AbstractMatrix,
atoms::Vector{<:DFTK.Element},
positions::Vector{<:AbstractVector};
@@ -687,18 +719,18 @@
kinetic_blowup,
kwargs...
) -> Model
-
Convenience constructor, which builds a standard atomic (kinetic + atomic potential) model. Use extra_terms to add additional terms.
sourceDFTK.mpi_nprocs — Functionmpi_nprocs() -> Int64
+
Convenience constructor, which builds a standard atomic (kinetic + atomic potential) model. Use extra_terms to add additional terms.
sourceDFTK.mpi_nprocs — Functionmpi_nprocs() -> Int64
mpi_nprocs(comm) -> Int64
-
Number of processors used in MPI. Can be called without ensuring initialization.
sourceDFTK.multiply_ψ_by_blochwave — Methodmultiply_ψ_by_blochwave(
+
Number of processors used in MPI. Can be called without ensuring initialization.
sourceDFTK.multiply_ψ_by_blochwave — Methodmultiply_ψ_by_blochwave(
basis::PlaneWaveBasis,
ψ,
f_real,
q
) -> Any
-
multiply_ψ_by_blochwave(basis::PlaneWaveBasis, ψ, f_real, q)
Return the Fourier coefficients for the Bloch waves $f^{\rm real}_{q} ψ_{k-q}$ in an element of basis.kpoints equivalent to $k-q$.
sourceDFTK.n_elec_core — Methodn_elec_core(el::DFTK.Element) -> Any
-
Return the number of core electrons
sourceDFTK.n_elec_valence — Methodn_elec_valence(el::DFTK.Element) -> Any
-
Return the number of valence electrons
sourceDFTK.n_electrons_from_atoms — Methodn_electrons_from_atoms(atoms) -> Any
-
Number of valence electrons.
sourceDFTK.newton — Methodnewton(
+
multiply_ψ_by_blochwave(basis::PlaneWaveBasis, ψ, f_real, q)
Return the Fourier coefficients for the Bloch waves $f^{\rm real}_{q} ψ_{k-q}$ in an element of basis.kpoints equivalent to $k-q$.
sourceDFTK.n_elec_core — Methodn_elec_core(el::DFTK.Element) -> Any
+
Return the number of core electrons
sourceDFTK.n_elec_valence — Methodn_elec_valence(el::DFTK.Element) -> Any
+
Return the number of valence electrons
sourceDFTK.n_electrons_from_atoms — Methodn_electrons_from_atoms(atoms) -> Any
+
Number of valence electrons.
sourceDFTK.newton — Methodnewton(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
ψ0;
tol,
@@ -706,21 +738,23 @@
maxiter,
callback,
is_converged
-) -> NamedTuple{(:ham, :basis, :energies, :converged, :ρ, :eigenvalues, :occupation, :εF, :n_iter, :ψ, :stage, :algorithm), _A} where _A<:Tuple{Hamiltonian, PlaneWaveBasis, Energies, Any, AbstractArray{_A, 4} where _A, Vector{Any}, Vector, Nothing, Int64, Any, Symbol, String}
+) -> NamedTuple{(:ham, :basis, :energies, :converged, :ρ, :eigenvalues, :occupation, :εF, :n_iter, :ψ, :stage, :algorithm, :runtime_ns), <:Tuple{Hamiltonian, PlaneWaveBasis, Energies, Any, AbstractArray{_A, 4} where _A, Vector{Any}, Vector, Nothing, Int64, Any, Symbol, String, UInt64}}
newton(basis::PlaneWaveBasis{T}, ψ0;
tol=1e-6, tol_cg=tol / 100, maxiter=20, callback=ScfDefaultCallback(),
- is_converged=ScfConvergenceDensity(tol))
Newton algorithm. Be careful that the starting point needs to be not too far from the solution.
sourceDFTK.next_compatible_fft_size — Methodnext_compatible_fft_size(
+ is_converged=ScfConvergenceDensity(tol))
Newton algorithm. Be careful that the starting point needs to be not too far from the solution.
sourceDFTK.next_compatible_fft_size — Methodnext_compatible_fft_size(
size::Int64;
smallprimes,
factors
) -> Int64
-
Find the next compatible FFT size Sizes must (a) be a product of small primes only and (b) contain the factors. If smallprimes is empty (a) is skipped.
sourceDFTK.next_density — Functionnext_density(
- ham::Hamiltonian
-) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), _A} where _A<:Tuple{Vector, Vector, Any, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), _A} where _A<:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}, Int64, Float64}
+
Find the next compatible FFT size Sizes must (a) be a product of small primes only and (b) contain the factors. If smallprimes is empty (a) is skipped.
sourceDFTK.next_density — Functionnext_density(
+ ham::Hamiltonian;
+ ...
+) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), <:Tuple{Vector, Vector, Vector, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), <:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}}, Int64, Float64}}
next_density(
ham::Hamiltonian,
- nbandsalg::DFTK.NbandsAlgorithm
-) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), _A} where _A<:Tuple{Vector, Vector, Any, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), _A} where _A<:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}, Int64, Any}
+ nbandsalg::DFTK.NbandsAlgorithm;
+ ...
+) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), <:Tuple{Vector, Vector, Vector, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), <:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}}, Int64, Any}}
next_density(
ham::Hamiltonian,
nbandsalg::DFTK.NbandsAlgorithm,
@@ -730,33 +764,33 @@
eigenvalues,
occupation,
kwargs...
-) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), _A} where _A<:Tuple{Vector, Vector, Any, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), _A} where _A<:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}, Int64, Any}
-
Obtain new density ρ by diagonalizing ham. Follows the policy imposed by the bands data structure to determine and adjust the number of bands to be computed.
sourceDFTK.norm2 — Methodnorm2(G) -> Any
-
Square of the ℓ²-norm.
sourceDFTK.norm_cplx — Methodnorm_cplx(x) -> Any
-
Complex-analytic extension of LinearAlgebra.norm(x) from real to complex inputs. Needed for phonons as we want to perform a matrix-vector product f'(x)·h, where f is a real-to-real function and h a complex vector. To do this using automatic differentiation, we can extend analytically f to accept complex inputs, then differentiate t -> f(x+t·h). This will fail if non-analytic functions like norm are used for complex inputs, and therefore we have to redefine it.
sourceDFTK.normalize_kpoint_coordinate — Methodnormalize_kpoint_coordinate(x::Real) -> Any
-
Bring $k$-point coordinates into the range [-0.5, 0.5)
sourceDFTK.overlap_Mmn_k_kpb — Methodoverlap_Mmn_k_kpb(
+) -> NamedTuple{(:ψ, :eigenvalues, :occupation, :εF, :ρout, :diagonalization, :n_bands_converge, :occupation_threshold), <:Tuple{Vector, Vector, Vector, Number, AbstractArray{_A, 4} where _A, NamedTuple{(:λ, :X, :residual_norms, :n_iter, :converged, :n_matvec), <:Tuple{Vector, Vector, Vector, Vector, Union{Missing, Bool}, Any}}, Int64, Any}}
+
Obtain new density ρ by diagonalizing ham. Follows the policy imposed by the bands data structure to determine and adjust the number of bands to be computed.
sourceDFTK.norm2 — Methodnorm2(G) -> Any
+
Square of the ℓ²-norm.
sourceDFTK.norm_cplx — Methodnorm_cplx(x) -> Any
+
Complex-analytic extension of LinearAlgebra.norm(x) from real to complex inputs. Needed for phonons as we want to perform a matrix-vector product f'(x)·h, where f is a real-to-real function and h a complex vector. To do this using automatic differentiation, we can extend analytically f to accept complex inputs, then differentiate t -> f(x+t·h). This will fail if non-analytic functions like norm are used for complex inputs, and therefore we have to redefine it.
sourceDFTK.normalize_kpoint_coordinate — Methodnormalize_kpoint_coordinate(x::Real) -> Any
+
Bring $k$-point coordinates into the range [-0.5, 0.5)
sourceDFTK.overlap_Mmn_k_kpb — Methodoverlap_Mmn_k_kpb(
basis::PlaneWaveBasis,
ψ,
ik,
- ikpb,
+ ik_plus_b,
G_shift,
n_bands
) -> Any
-
Computes the matrix $[M^{k,b}]_{m,n} = \langle u_{m,k} | u_{n,k+b} \rangle$ for given k, kpb = $k+b$.
G_shift is the "shifting" vector, correction due to the periodicity conditions imposed on $k \to ψ_k$. It is non zero if kpb is taken in another unit cell of the reciprocal lattice. We use here that: $u_{n(k + G_{\rm shift})}(r) = e^{-i*\langle G_{\rm shift},r \rangle} u_{nk}$.
sourceDFTK.phonon_modes — Methodphonon_modes(
+
Computes the matrix $[M^{k,b}]_{m,n} = \langle u_{m,k} | u_{n,k+b} \rangle$ for given k.
G_shift is the "shifting" vector, correction due to the periodicity conditions imposed on $k \to ψ_k$. It is non zero if k_plus_b is taken in another unit cell of the reciprocal lattice. We use here that: $u_{n(k + G_{\rm shift})}(r) = e^{-i*\langle G_{\rm shift},r \rangle} u_{nk}$.
sourceDFTK.pcut_psp_local — Methodpcut_psp_local(psp::PspHgh{T}) -> Any
+
Estimate an upper bound for the argument p after which abs(eval_psp_local_fourier(psp, p)) is a strictly decreasing function.
sourceDFTK.pcut_psp_projector — Methodpcut_psp_projector(psp::PspHgh{T}, i, l) -> Any
+
Estimate an upper bound for the argument p after which eval_psp_projector_fourier(psp, p) is a strictly decreasing function.
sourceDFTK.phonon_modes — Methodphonon_modes(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
dynmat
-) -> NamedTuple{(:frequencies, :vectors), _A} where _A<:Tuple{Any, Any}
-
Solve the eigenproblem for a dynamical matrix: returns the frequencies and eigenvectors (vectors).
sourceDFTK.plot_bandstructure — FunctionCompute and plot the band structure. Kwargs are like in compute_bands. Requires Plots.jl to be loaded to be defined and working properly. The unit used to plot the bands can be selected using the unit parameter. Like in the rest of DFTK Hartree is used by default. Another standard choices is unit=u"eV" (electron volts).
sourceDFTK.plot_dos — FunctionPlot the density of states over a reasonable range. Requires to load Plots.jl beforehand.
sourceDFTK.psp_local_polynomial — Functionpsp_local_polynomial(T, psp::PspHgh) -> Any
+) -> NamedTuple{(:frequencies, :vectors), <:Tuple{Any, Any}}
+
Solve the eigenproblem for a dynamical matrix: returns the frequencies and eigenvectors (vectors).
sourceDFTK.plot_bandstructure — FunctionCompute and plot the band structure. Kwargs are like in compute_bands. Requires Plots.jl to be loaded to be defined and working properly. The unit used to plot the bands can be selected using the unit parameter. Like in the rest of DFTK Hartree is used by default. Another standard choices is unit=u"eV" (electron volts).
sourceDFTK.plot_dos — FunctionPlot the density of states over a reasonable range. Requires to load Plots.jl beforehand.
sourceDFTK.psp_local_polynomial — Functionpsp_local_polynomial(T, psp::PspHgh) -> Any
psp_local_polynomial(T, psp::PspHgh, t) -> Any
-
The local potential of a HGH pseudopotentials in reciprocal space can be brought to the form $Q(t) / (t^2 exp(t^2 / 2))$ where $t = r_\text{loc} q$ and Q is a polynomial of at most degree 8. This function returns Q.
sourceDFTK.psp_projector_polynomial — Functionpsp_projector_polynomial(T, psp::PspHgh, i, l) -> Any
+
The local potential of a HGH pseudopotentials in reciprocal space can be brought to the form $Q(t) / (t^2 exp(t^2 / 2))$ where $t = r_\text{loc} p$ and Q is a polynomial of at most degree 8. This function returns Q.
sourceDFTK.psp_projector_polynomial — Functionpsp_projector_polynomial(T, psp::PspHgh, i, l) -> Any
psp_projector_polynomial(T, psp::PspHgh, i, l, t) -> Any
-
The nonlocal projectors of a HGH pseudopotentials in reciprocal space can be brought to the form $Q(t) exp(-t^2 / 2)$ where $t = r_l q$ and Q is a polynomial. This function returns Q.
sourceDFTK.qcut_psp_local — Methodqcut_psp_local(psp::PspHgh{T}) -> Any
-
Estimate an upper bound for the argument q after which abs(eval_psp_local_fourier(psp, q)) is a strictly decreasing function.
sourceDFTK.qcut_psp_projector — Methodqcut_psp_projector(psp::PspHgh{T}, i, l) -> Any
-
Estimate an upper bound for the argument q after which eval_psp_projector_fourier(psp, q) is a strictly decreasing function.
sourceDFTK.r_vectors — Methodr_vectors(
+
The nonlocal projectors of a HGH pseudopotentials in reciprocal space can be brought to the form $Q(t) exp(-t^2 / 2)$ where $t = r_l p$ and Q is a polynomial. This function returns Q.
sourceDFTK.r_vectors — Methodr_vectors(
basis::PlaneWaveBasis
) -> AbstractArray{StaticArraysCore.SVector{3, VT}, 3} where VT<:Real
-
r_vectors(basis::PlaneWaveBasis)
The list of $r$ vectors, in reduced coordinates. By convention, this is in [0,1)^3.
sourceDFTK.r_vectors_cart — Methodr_vectors_cart(basis::PlaneWaveBasis) -> Any
-
r_vectors_cart(basis::PlaneWaveBasis)
The list of $r$ vectors, in cartesian coordinates.
sourceDFTK.radial_hydrogenic — Methodradial_hydrogenic(
+
r_vectors(basis::PlaneWaveBasis)
The list of $r$ vectors, in reduced coordinates. By convention, this is in [0,1)^3.
sourceDFTK.r_vectors_cart — Methodr_vectors_cart(basis::PlaneWaveBasis) -> Any
+
r_vectors_cart(basis::PlaneWaveBasis)
The list of $r$ vectors, in cartesian coordinates.
sourceDFTK.radial_hydrogenic — Methodradial_hydrogenic(
r::AbstractArray{T<:Real, 1},
n::Integer
) -> Any
@@ -765,44 +799,58 @@
n::Integer,
α::Real
) -> Any
-
Radial functions from solutions of Hydrogenic Schrödinger equation. Same as Wannier90 user guide Table 3.3.
Arguments
r: radial gridn: principal quantum numberα: diffusivity, $\frac{Z}/{a}$ where $Z$ is the atomic number and $a$ is the Bohr radius.
sourceDFTK.random_density — Methodrandom_density(
+
Radial functions from solutions of Hydrogenic Schrödinger equation. Same as Wannier90 user guide Table 3.3.
Arguments
r: radial gridn: principal quantum numberα: diffusivity, $\frac{Z}{a}$ where $Z$ is the atomic number and $a$ is the Bohr radius.
sourceDFTK.random_density — Methodrandom_density(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
n_electrons::Integer
) -> Any
-
Build a random charge density normalized to the provided number of electrons.
sourceDFTK.read_w90_nnkp — Methodread_w90_nnkp(
+
Build a random charge density normalized to the provided number of electrons.
sourceDFTK.read_w90_nnkp — Methodread_w90_nnkp(
fileprefix::String
-) -> NamedTuple{(:nntot, :nnkpts), Tuple{Int64, Vector{NamedTuple{(:ik, :ikpb, :G_shift), Tuple{Int64, Int64, Vector{Int64}}}}}}
-
Read the .nnkp file provided by the preprocessing routine of Wannier90 (i.e. "wannier90.x -pp prefix") Returns:
- the array 'nnkpts' of k points, their respective nearest neighbors and associated shifing vectors (non zero if the neighbor is located in another cell).
- the number 'nntot' of neighbors per k point.
TODO: add the possibility to exclude bands
sourceDFTK.reducible_kcoords — Methodreducible_kcoords(
+) -> @NamedTuple{nntot::Int64, nnkpts::Vector{@NamedTuple{ik::Int64, ik_plus_b::Int64, G_shift::Vector{Int64}}}}
+
Read the .nnkp file provided by the preprocessing routine of Wannier90 (i.e. "wannier90.x -pp prefix") Returns:
- the array 'nnkpts' of k points, their respective nearest neighbors and associated shifing vectors (non zero if the neighbor is located in another cell).
- the number 'nntot' of neighbors per k point.
TODO: add the possibility to exclude bands
sourceDFTK.reducible_kcoords — Methodreducible_kcoords(
kgrid::MonkhorstPack
-) -> NamedTuple{(:kcoords,), Tuple{Vector{StaticArraysCore.SVector{3, Rational{Int64}}}}}
-
Construct the coordinates of the k-points in a (shifted) Monkhorst-Pack grid
sourceDFTK.run_wannier90 — FunctionWannerize the obtained bands using wannier90. By default all converged bands from the scfres are employed (change with n_bands kwargs) and n_wannier = n_bands wannier functions are computed. Random Gaussians are used as guesses by default, can be changed using the projections kwarg. All keyword arguments supported by Wannier90 for the disentanglement may be added as keyword arguments. The function returns the fileprefix.
Experimental feature Currently this is an experimental feature, which has not yet been tested to full depth. The interface is considered unstable and may change incompatibly in the future. Use at your own risk and please report bugs in case you encounter any.
sourceDFTK.save_bands — Methodsave_bands(
+) -> @NamedTuple{kcoords::Vector{StaticArraysCore.SVector{3, Rational{Int64}}}}
+
Construct the coordinates of the k-points in a (shifted) Monkhorst-Pack grid
sourceDFTK.run_wannier90 — FunctionWannerize the obtained bands using wannier90. By default all converged bands from the scfres are employed (change with n_bands kwargs) and n_wannier = n_bands wannier functions are computed. Random Gaussians are used as guesses by default, can be changed using the projections kwarg. All keyword arguments supported by Wannier90 for the disentanglement may be added as keyword arguments. The function returns the fileprefix.
Experimental feature Currently this is an experimental feature, which has not yet been tested to full depth. The interface is considered unstable and may change incompatibly in the future. Use at your own risk and please report bugs in case you encounter any.
sourceDFTK.save_bands — Methodsave_bands(
filename::AbstractString,
band_data::NamedTuple;
- save_ψ,
- kwargs...
+ save_ψ
)
-
Write the computed bands to a file. save_ψ determines whether the wavefunction is also saved or not. Note that this function can be both used on the results of compute_bands and self_consistent_field.
sourceDFTK.save_scfres — Methodsave_scfres(
+
Write the computed bands to a file. On all processes, but the master one the filename is ignored. save_ψ determines whether the wavefunction is also saved or not. Note that this function can be both used on the results of compute_bands and self_consistent_field.
Changes to data format reserved No guarantees are made with respect to the format of the keys at this point. We may change this incompatibly between DFTK versions (including patch versions). In particular changes with respect to the ψ structure are planned.
sourceDFTK.save_scfres — Methodsave_scfres(
filename::AbstractString,
scfres::NamedTuple;
- kwargs...
+ save_ψ,
+ extra_data,
+ compress,
+ save_ρ
) -> Any
-
save_scfres(filename, scfres)
Save an scfres obtained from self_consistent_field to a file. The format is determined from the file extension. Currently the following file extensions are recognized and supported:
- jld2: A JLD2 file. Stores the complete state and can be used (with
load_scfres) to restart an SCF from a checkpoint or post-process an SCF solution. See Saving SCF results on disk and SCF checkpoints for details. - vts: A VTK file for visualisation e.g. in paraview. Stores the density, spin density and some metadata (energy, Fermi level, occupation etc.). Supports these keyword arguments:
save_ψ: Save the real-space representation of the orbitals as well (may lead to larger files).extra_data: Dict{String,Array} with additional data on the 3D real-space grid to store into the VTK file.
- json: A JSON file with basic information about the SCF run. Stores for example the number of iterations, occupations, norm of the most recent density change, eigenvalues, Fermi level etc.
No compatibility guarantees No guarantees are made with respect to this function at this point. It may change incompatibly between DFTK versions or stop working / be removed in the future.
sourceDFTK.scf_anderson_solver — Functionscf_anderson_solver(
-
-) -> DFTK.var"#anderson#650"{DFTK.var"#anderson#649#651"{Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Int64}}
-scf_anderson_solver(m; kwargs...) -> DFTK.var"#anderson#650"
-
Create a simple anderson-accelerated SCF solver. m specifies the number of steps to keep the history of.
sourceDFTK.scf_damping_quadratic_model — Methodscf_damping_quadratic_model(
+
Save an scfres obtained from self_consistent_field to a file. On all processes but the master one the filename is ignored. The format is determined from the file extension. Currently the following file extensions are recognized and supported:
- jld2: A JLD2 file. Stores the complete state and can be used (with
load_scfres) to restart an SCF from a checkpoint or post-process an SCF solution. Note that this file is also a valid HDF5 file, which can thus similarly be read by external non-Julia libraries such as h5py or similar. See Saving SCF results on disk and SCF checkpoints for details. - vts: A VTK file for visualisation e.g. in paraview. Stores the density, spin density, optionally bands and some metadata.
- json: A JSON file with basic information about the SCF run. Stores for example the number of iterations, occupations, some information about the basis, eigenvalues, Fermi level etc.
Keyword arguments:
save_ψ: Save the orbitals as well (may lead to larger files). This is the default for jld2, but false for all other formats, where this is considerably more expensive.save_ρ: Save the density as well (may lead to larger files). This is the default for all but json.extra_data: Additional data to place into the file. The data is just copied like fp["key"] = value, where fp is a JLD2.JLDFile, WriteVTK.vtk_grid and so on.compress: Apply compression to array data. Requires the CodecZlib package to be available.
Changes to data format reserved No guarantees are made with respect to the format of the keys at this point. We may change this incompatibly between DFTK versions (including patch versions). In particular changes with respect to the ψ structure are planned.
sourceDFTK.scatter_kpts_block — Methodscatter_kpts_block(
+ basis::PlaneWaveBasis,
+ data::Union{Nothing, AbstractArray}
+) -> Any
+
Scatter the data of a quantity depending on k-Points from the master process to the child processes and return it as a Vector{Array}, where the outer vector is a list over all k-points. On non-master processes nothing may be passed.
sourceDFTK.scf_anderson_solver — Functionscf_anderson_solver(
+;
+ ...
+) -> DFTK.var"#anderson#695"{DFTK.var"#anderson#694#696"{Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, Int64}}
+scf_anderson_solver(
+ m;
+ kwargs...
+) -> DFTK.var"#anderson#695"{DFTK.var"#anderson#694#696"{Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, _A}} where _A
+
Create a simple anderson-accelerated SCF solver. m specifies the number of steps to keep the history of.
sourceDFTK.scf_damping_quadratic_model — Methodscf_damping_quadratic_model(
info,
info_next;
modeltol
-) -> NamedTuple{(:α, :relerror), _A} where _A<:Tuple{Any, Any}
-
Use the two iteration states info and info_next to find a damping value from a quadratic model for the SCF energy. Returns nothing if the constructed model is not considered trustworthy, else returns the suggested damping.
sourceDFTK.scf_damping_solver — Functionscf_damping_solver(
+) -> NamedTuple{(:α, :relerror), <:Tuple{Any, Any}}
+
Use the two iteration states info and info_next to find a damping value from a quadratic model for the SCF energy. Returns nothing if the constructed model is not considered trustworthy, else returns the suggested damping.
sourceDFTK.scf_damping_solver — Functionscf_damping_solver(
-) -> DFTK.var"#fp_solver#646"{DFTK.var"#fp_solver#645#647"}
+) -> DFTK.var"#fp_solver#691"{DFTK.var"#fp_solver#690#692"}
scf_damping_solver(
β
-) -> DFTK.var"#fp_solver#646"{DFTK.var"#fp_solver#645#647"}
-
Create a damped SCF solver updating the density as x = β * x_new + (1 - β) * x
sourceDFTK.select_eigenpairs_all_kblocks — Methodselect_eigenpairs_all_kblocks(eigres, range) -> Any
-
Function to select a subset of eigenpairs on each $k$-Point. Works on the Tuple returned by diagonalize_all_kblocks.
sourceDFTK.self_consistent_field — Methodself_consistent_field(
+) -> DFTK.var"#fp_solver#691"{DFTK.var"#fp_solver#690#692"}
+
Create a damped SCF solver updating the density as x = β * x_new + (1 - β) * x
sourceDFTK.scfres_to_dict — Methodscfres_to_dict(
+ scfres::NamedTuple;
+ kwargs...
+) -> Dict{String, Any}
+
Convert an scfres to a dictionary representation. Intended to give a condensed set of results and useful metadata for post processing. See also the todict function for the Model and the PlaneWaveBasis as well as the band_data_to_dict functions, which are called by this function and their outputs merged. Only the master process returns meaningful data.
Some details on the conventions for the returned data:
- ρ: (fftsize[1], fftsize[2], fftsize[3], nspin) array of density on real-space grid.
- energies: Dictionary / subdirectory containing the energy terms
- converged: Has the SCF reached convergence
- norm_Δρ: Most recent change in ρ during an SCF step
- occupation_threshold: Threshold below which orbitals are considered unoccupied
- nbandsconverge: Number of bands that have been fully converged numerically.
- n_iter: Number of iterations.
sourceDFTK.select_eigenpairs_all_kblocks — Methodselect_eigenpairs_all_kblocks(eigres, range) -> NamedTuple
+
Function to select a subset of eigenpairs on each $k$-Point. Works on the Tuple returned by diagonalize_all_kblocks.
sourceDFTK.self_consistent_field — Methodself_consistent_field(
basis::PlaneWaveBasis{T, VT} where VT<:Real;
ρ,
ψ,
@@ -813,24 +861,24 @@
damping,
solver,
eigensolver,
- determine_diagtol,
+ diagtolalg,
nbandsalg,
fermialg,
callback,
compute_consistent_energies,
response
-) -> NamedTuple{(:ham, :basis, :energies, :ρ, :eigenvalues, :occupation, :εF, :ψ, :response, :converged, :occupation_threshold, :α, :n_iter, :n_bands_converge, :diagonalization, :stage, :algorithm, :norm_Δρ), _A} where _A<:Tuple{Hamiltonian, PlaneWaveBasis{T, VT} where {T<:ForwardDiff.Dual, VT<:Real}, Energies, Vararg{Any, 15}}
-
self_consistent_field(basis; [tol, mixing, damping, ρ, ψ])
Solve the Kohn-Sham equations with a density-based SCF algorithm using damped, preconditioned iterations where $ρ_\text{next} = α P^{-1} (ρ_\text{out} - ρ_\text{in})$.
Overview of parameters:
ρ: Initial densityψ: Initial orbitalstol: Tolerance for the density change ($\|ρ_\text{out} - ρ_\text{in}\|$) to flag convergence. Default is 1e-6.is_converged: Convergence control callback. Typical objects passed here are DFTK.ScfConvergenceDensity(tol) (the default), DFTK.ScfConvergenceEnergy(tol) or DFTK.ScfConvergenceForce(tol).maxiter: Maximal number of SCF iterationsmixing: Mixing method, which determines the preconditioner $P^{-1}$ in the above equation. Typical mixings are LdosMixing, KerkerMixing, SimpleMixing or DielectricMixing. Default is LdosMixing()damping: Damping parameter $α$ in the above equation. Default is 0.8.nbandsalg: By default DFTK uses nbandsalg=AdaptiveBands(model), which adaptively determines the number of bands to compute. If you want to influence this algorithm or use a predefined number of bands in each SCF step, pass a FixedBands or AdaptiveBands. Beware that with non-zero temperature, the convergence of the SCF algorithm may be limited by the default_occupation_threshold() parameter. For highly accurate calculations we thus recommend increasing the occupation_threshold of the AdaptiveBands.callback: Function called at each SCF iteration. Usually takes care of printing the intermediate state.
sourceDFTK.simpson — Functionsimpson(x, y)
Integrate y(x) over x using Simpson's method quadrature.
sourceDFTK.sin2pi — Methodsin2pi(x) -> Any
-
Function to compute sin(2π x)
sourceDFTK.solve_ΩplusK — Methodsolve_ΩplusK(
+) -> NamedTuple{(:ham, :basis, :energies, :ρ, :eigenvalues, :occupation, :εF, :ψ, :response, :converged, :occupation_threshold, :α, :n_iter, :n_bands_converge, :diagonalization, :stage, :algorithm, :runtime_ns), <:Tuple{Hamiltonian, PlaneWaveBasis{T, VT} where {T<:ForwardDiff.Dual, VT<:Real}, Energies, Vararg{Any, 15}}}
+
self_consistent_field(basis; [tol, mixing, damping, ρ, ψ])
Solve the Kohn-Sham equations with a density-based SCF algorithm using damped, preconditioned iterations where $ρ_\text{next} = α P^{-1} (ρ_\text{out} - ρ_\text{in})$.
Overview of parameters:
ρ: Initial densityψ: Initial orbitalstol: Tolerance for the density change ($\|ρ_\text{out} - ρ_\text{in}\|$) to flag convergence. Default is 1e-6.is_converged: Convergence control callback. Typical objects passed here are ScfConvergenceDensity(tol) (the default), ScfConvergenceEnergy(tol) or ScfConvergenceForce(tol).maxiter: Maximal number of SCF iterationsmixing: Mixing method, which determines the preconditioner $P^{-1}$ in the above equation. Typical mixings are LdosMixing, KerkerMixing, SimpleMixing or DielectricMixing. Default is LdosMixing()damping: Damping parameter $α$ in the above equation. Default is 0.8.nbandsalg: By default DFTK uses nbandsalg=AdaptiveBands(model), which adaptively determines the number of bands to compute. If you want to influence this algorithm or use a predefined number of bands in each SCF step, pass a FixedBands or AdaptiveBands. Beware that with non-zero temperature, the convergence of the SCF algorithm may be limited by the default_occupation_threshold() parameter. For highly accurate calculations we thus recommend increasing the occupation_threshold of the AdaptiveBands.callback: Function called at each SCF iteration. Usually takes care of printing the intermediate state.
sourceDFTK.simpson — Functionsimpson(x, y)
Integrate y(x) over x using Simpson's method quadrature.
sourceDFTK.sin2pi — Methodsin2pi(x) -> Any
+
Function to compute sin(2π x)
sourceDFTK.solve_ΩplusK — Methodsolve_ΩplusK(
basis::PlaneWaveBasis{T, VT} where VT<:Real,
ψ,
rhs,
occupation;
callback,
tol
-) -> NamedTuple{(:δψ, :converged, :tol, :residual_norm, :n_iter), _A} where _A<:Tuple{Any, Bool, Any, Any, Int64}
+) -> NamedTuple{(:δψ, :converged, :tol, :residual_norm, :n_iter), <:Tuple{Any, Bool, Float64, Any, Int64}}
solve_ΩplusK(basis::PlaneWaveBasis{T}, ψ, res, occupation;
- tol=1e-10, verbose=false) where {T}
Return δψ where (Ω+K) δψ = rhs
sourceDFTK.solve_ΩplusK_split — Methodsolve_ΩplusK_split(
+ tol=1e-10, verbose=false) where {T}
Return δψ where (Ω+K) δψ = rhs
sourceDFTK.solve_ΩplusK_split — Methodsolve_ΩplusK_split(
ham::Hamiltonian,
ρ::AbstractArray{T},
ψ,
@@ -845,11 +893,12 @@
q,
kwargs...
)
-
Solve the problem (Ω+K) δψ = rhs using a split algorithm, where rhs is typically -δHextψ (the negative matvec of an external perturbation with the SCF orbitals ψ) and δψ is the corresponding total variation in the orbitals ψ. Additionally returns: - δρ: Total variation in density) - δHψ: Total variation in Hamiltonian applied to orbitals - δeigenvalues: Total variation in eigenvalues - δVind: Change in potential induced by δρ (the term needed on top of δHextψ to get δHψ).
sourceDFTK.spglib_standardize_cell — Methodspglib_standardize_cell(
+
Solve the problem (Ω+K) δψ = rhs using a split algorithm, where rhs is typically -δHextψ (the negative matvec of an external perturbation with the SCF orbitals ψ) and δψ is the corresponding total variation in the orbitals ψ. Additionally returns: - δρ: Total variation in density) - δHψ: Total variation in Hamiltonian applied to orbitals - δeigenvalues: Total variation in eigenvalues - δVind: Change in potential induced by δρ (the term needed on top of δHextψ to get δHψ).
sourceDFTK.spglib_standardize_cell — Methodspglib_standardize_cell(
lattice::AbstractArray{T},
atom_groups,
- positions
-) -> NamedTuple{(:lattice, :atom_groups, :positions, :magnetic_moments), _A} where _A<:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}
+ positions;
+ ...
+) -> NamedTuple{(:lattice, :atom_groups, :positions, :magnetic_moments), <:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}}
spglib_standardize_cell(
lattice::AbstractArray{T},
atom_groups,
@@ -858,38 +907,40 @@
correct_symmetry,
primitive,
tol_symmetry
-) -> NamedTuple{(:lattice, :atom_groups, :positions, :magnetic_moments), _A} where _A<:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}
-
Returns crystallographic conventional cell according to the International Table of Crystallography Vol A (ITA) in case primitive=false. If primitive=true the primitive lattice is returned in the convention of the reference work of Cracknell, Davies, Miller, and Love (CDML). Of note this has minor differences to the primitive setting choice made in the ITA.
sourceDFTK.sphericalbesselj_fast — Methodsphericalbesselj_fast(l::Integer, x) -> Any
-
sphericalbesselj_fast(l::Integer, x::Number)
Returns the spherical Bessel function of the first kind jl(x). Consistent with https://en.wikipedia.org/wiki/Besselfunction#SphericalBesselfunctions and with SpecialFunctions.sphericalbesselj. Specialized for integer 0 <= l <= 5.
sourceDFTK.spin_components — Methodspin_components(
+) -> NamedTuple{(:lattice, :atom_groups, :positions, :magnetic_moments), <:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}}
+
Returns crystallographic conventional cell according to the International Table of Crystallography Vol A (ITA) in case primitive=false. If primitive=true the primitive lattice is returned in the convention of the reference work of Cracknell, Davies, Miller, and Love (CDML). Of note this has minor differences to the primitive setting choice made in the ITA.
sourceDFTK.sphericalbesselj_fast — Methodsphericalbesselj_fast(l::Integer, x) -> Any
+
sphericalbesselj_fast(l::Integer, x::Number)
Returns the spherical Bessel function of the first kind jl(x). Consistent with [wikipedia](https://en.wikipedia.org/wiki/Besselfunction#SphericalBesselfunctions) and with SpecialFunctions.sphericalbesselj. Specialized for integer 0 <= l <= 5.
sourceDFTK.spin_components — Methodspin_components(
spin_polarization::Symbol
) -> Union{Bool, Tuple{Symbol}, Tuple{Symbol, Symbol}}
-
Explicit spin components of the KS orbitals and the density
sourceDFTK.split_evenly — Methodsplit_evenly(itr, N) -> Any
-
Split an iterable evenly into N chunks, which will be returned.
sourceDFTK.standardize_atoms — Functionstandardize_atoms(
+
Explicit spin components of the KS orbitals and the density
sourceDFTK.split_evenly — Methodsplit_evenly(itr, N) -> Any
+
Split an iterable evenly into N chunks, which will be returned.
sourceDFTK.standardize_atoms — Functionstandardize_atoms(
lattice,
atoms,
- positions
-) -> NamedTuple{(:lattice, :atoms, :positions, :magnetic_moments), _A} where _A<:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}
+ positions;
+ ...
+) -> NamedTuple{(:lattice, :atoms, :positions, :magnetic_moments), <:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}}
standardize_atoms(
lattice,
atoms,
positions,
magnetic_moments;
kwargs...
-) -> NamedTuple{(:lattice, :atoms, :positions, :magnetic_moments), _A} where _A<:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}
-
Apply various standardisations to a lattice and a list of atoms. It uses spglib to detect symmetries (within tol_symmetry), then cleans up the lattice according to the symmetries (unless correct_symmetry is false) and returns the resulting standard lattice and atoms. If primitive is true (default) the primitive unit cell is returned, else the conventional unit cell is returned.
sourceDFTK.symmetries_preserving_kgrid — Methodsymmetries_preserving_kgrid(symmetries, kcoords) -> Any
-
Filter out the symmetry operations that don't respect the symmetries of the discrete BZ grid
sourceDFTK.symmetries_preserving_rgrid — Methodsymmetries_preserving_rgrid(symmetries, fft_size) -> Any
-
Filter out the symmetry operations that don't respect the symmetries of the discrete real-space grid
sourceDFTK.symmetrize_forces — Methodsymmetrize_forces(model::Model, forces; symmetries)
-
Symmetrize the forces in reduced coordinates, forces given as an array forces[iel][α,i]
sourceDFTK.symmetrize_stresses — Methodsymmetrize_stresses(model::Model, stresses; symmetries)
-
Symmetrize the stress tensor, given as a Matrix in cartesian coordinates
sourceDFTK.symmetrize_ρ — Methodsymmetrize_ρ(
+) -> NamedTuple{(:lattice, :atoms, :positions, :magnetic_moments), <:Tuple{Matrix, Any, Any, Vector{StaticArraysCore.SVector{3, Float64}}}}
+
Apply various standardisations to a lattice and a list of atoms. It uses spglib to detect symmetries (within tol_symmetry), then cleans up the lattice according to the symmetries (unless correct_symmetry is false) and returns the resulting standard lattice and atoms. If primitive is true (default) the primitive unit cell is returned, else the conventional unit cell is returned.
sourceDFTK.symmetries_preserving_kgrid — Methodsymmetries_preserving_kgrid(symmetries, kcoords) -> Any
+
Filter out the symmetry operations that don't respect the symmetries of the discrete BZ grid
sourceDFTK.symmetries_preserving_rgrid — Methodsymmetries_preserving_rgrid(symmetries, fft_size) -> Any
+
Filter out the symmetry operations that don't respect the symmetries of the discrete real-space grid
sourceDFTK.symmetrize_forces — Methodsymmetrize_forces(model::Model, forces; symmetries)
+
Symmetrize the forces in reduced coordinates, forces given as an array forces[iel][α,i].
sourceDFTK.symmetrize_stresses — Methodsymmetrize_stresses(model::Model, stresses; symmetries)
+
Symmetrize the stress tensor, given as a Matrix in cartesian coordinates
sourceDFTK.symmetrize_ρ — Methodsymmetrize_ρ(
basis,
ρ::AbstractArray{T};
symmetries,
do_lowpass
) -> Any
-
Symmetrize a density by applying all the basis (by default) symmetries and forming the average.
sourceDFTK.symmetry_operations — Functionsymmetry_operations(
+
Symmetrize a density by applying all the basis (by default) symmetries and forming the average.
sourceDFTK.symmetry_operations — Functionsymmetry_operations(
lattice,
atoms,
- positions
+ positions;
+ ...
) -> Union{Vector{SymOp{Bool}}, Vector{SymOp{Float64}}}
symmetry_operations(
lattice,
@@ -899,63 +950,63 @@
tol_symmetry,
check_symmetry
) -> Union{Vector{SymOp{Bool}}, Vector{SymOp{Float64}}}
-
Return the symmetries given an atomic structure with optionally designated magnetic moments on each of the atoms. The symmetries are determined using spglib.
sourceDFTK.symmetry_operations — Methodsymmetry_operations(
+
Return the symmetries given an atomic structure with optionally designated magnetic moments on each of the atoms. The symmetries are determined using spglib.
sourceDFTK.symmetry_operations — Methodsymmetry_operations(
hall_number::Integer
) -> Vector{SymOp{Float64}}
-
Return the Symmetry operations given a hall_number.
This function allows to directly access to the space group operations in the spglib database. To specify the space group type with a specific choice, hall_number is used.
The definition of hall_number is found at Space group type.
sourceDFTK.synchronize_device — Methodsynchronize_device(_::DFTK.AbstractArchitecture)
-
Synchronize data and finish all operations on the execution stream of the device. This needs to be called explicitly before a task finishes (e.g. in an @spawn block).
sourceDFTK.to_cpu — Methodto_cpu(x::AbstractArray) -> Array
-
Transfer an array from a device (typically a GPU) to the CPU.
sourceDFTK.to_device — Methodto_device(_::DFTK.CPU, x) -> Any
-
Transfer an array to a particular device (typically a GPU)
sourceDFTK.todict — Methodtodict(energies::Energies) -> Dict{String}
-
Convert an Energies struct to a dictionary representation
sourceDFTK.todict — Methodtodict(model::Model) -> Dict
-
Convert a Model struct to a dictionary representation. Intended to give a condensed set of useful metadata to post-processing scripts or for storing computational results (e.g. bands, bloch waves etc.).
Some details on the conventions for the returned data:
- lattice, recip_lattice: Always a zero-padded 3x3 matrix, independent on the actual dimension
- atomicpositions, atomicpositions_cart: Atom positions in fractional or cartesian coordinates, respectively.
- atomic_symbols: Atomic symbols if known.
- terms: Some rough information on the terms used for the computation.
- n_electrons: Number of electrons, may be missing if εF is fixed instead
- εF: Fixed Fermi level to use, may be missing if n_electronis is specified instead.
sourceDFTK.todict — Methodtodict(basis::PlaneWaveBasis) -> Dict
-
Convert a PlaneWaveBasis struct to a dictionary representation. Intended to give a condensed set of useful metadata to post-processing scripts or for storing computational results (e.g. bands, bloch waves etc.). As such the function is lossy and might not keep all data consistently. Returns the same result on all MPI processors. See also the todict function for the Model, which is called from this one to merge the data of both outputs.
Some details on the conventions for the returned data:
- dvol: Volume element for real-space integration
- variational: Is the k-point specific basis (for ψ) variationally consistent with the basis for ρ.
- kweights: Weights for the k-points, summing to 1.0
sourceDFTK.total_local_potential — Methodtotal_local_potential(ham::Hamiltonian) -> Any
-
Get the total local potential of the given Hamiltonian, in real space in the spin components.
sourceDFTK.transfer_blochwave — Methodtransfer_blochwave(
+
Return the Symmetry operations given a hall_number.
This function allows to directly access to the space group operations in the spglib database. To specify the space group type with a specific choice, hall_number is used.
The definition of hall_number is found at Space group type.
sourceDFTK.synchronize_device — Methodsynchronize_device(_::DFTK.AbstractArchitecture)
+
Synchronize data and finish all operations on the execution stream of the device. This needs to be called explicitly before a task finishes (e.g. in an @spawn block).
sourceDFTK.to_cpu — Methodto_cpu(x::AbstractArray) -> Array
+
Transfer an array from a device (typically a GPU) to the CPU.
sourceDFTK.to_device — Methodto_device(_::DFTK.CPU, x) -> Any
+
Transfer an array to a particular device (typically a GPU)
sourceDFTK.todict — Methodtodict(energies::Energies) -> Dict
+
Convert an Energies struct to a dictionary representation
sourceDFTK.todict — Methodtodict(model::Model) -> Dict{String, Any}
+
Convert a Model struct to a dictionary representation. Intended to give a condensed set of useful metadata to post-processing scripts or for storing computational results (e.g. bands, bloch waves etc.).
Some details on the conventions for the returned data:
- lattice, recip_lattice: Always a zero-padded 3x3 matrix, independent on the actual dimension
- atomicpositions, atomicpositions_cart: Atom positions in fractional or cartesian coordinates, respectively.
- atomic_symbols: Atomic symbols if known.
- terms: Some rough information on the terms used for the computation.
- n_electrons: Number of electrons, may be missing if εF is fixed instead
- εF: Fixed Fermi level to use, may be missing if n_electronis is specified instead.
sourceDFTK.todict — Methodtodict(basis::PlaneWaveBasis) -> Dict{String, Any}
+
Convert a PlaneWaveBasis struct to a dictionary representation. Intended to give a condensed set of useful metadata to post-processing scripts or for storing computational results (e.g. bands, bloch waves etc.). As such the function is lossy and might not keep all data consistently. Returns the same result on all MPI processors. See also the todict function for the Model, which is called from this one to merge the data of both outputs.
Some details on the conventions for the returned data:
- dvol: Volume element for real-space integration
- variational: Is the k-point specific basis (for ψ) variationally consistent with the basis for ρ.
- kweights: Weights for the k-points, summing to 1.0
sourceDFTK.total_local_potential — Methodtotal_local_potential(ham::Hamiltonian) -> Any
+
Get the total local potential of the given Hamiltonian, in real space in the spin components.
sourceDFTK.transfer_blochwave — Methodtransfer_blochwave(
ψ_in,
- basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
- basis_out::PlaneWaveBasis{T, VT} where VT<:Real
-) -> Any
-
Transfer Bloch wave between two basis sets. Limited feature set.
sourceDFTK.transfer_blochwave_kpt — Methodtransfer_blochwave_kpt(
+ basis_in::PlaneWaveBasis,
+ basis_out::PlaneWaveBasis
+) -> Vector
+
Transfer Bloch wave between two basis sets. Limited feature set.
sourceDFTK.transfer_blochwave_kpt — Methodtransfer_blochwave_kpt(
ψk_in,
basis::PlaneWaveBasis,
kpt_in,
kpt_out,
ΔG
) -> Any
-
Transfer an array ψk_in expanded on kpt_in, and produce $ψ(r) e^{i ΔG·r}$ expanded on kpt_out. It is mostly useful for phonons. Beware: ψk_out can lose information if the shift ΔG is large or if the G_vectors differ between k-points.
sourceDFTK.transfer_blochwave_kpt — Methodtransfer_blochwave_kpt(
+
Transfer an array ψk_in expanded on kpt_in, and produce $ψ(r) e^{i ΔG·r}$ expanded on kpt_out. It is mostly useful for phonons. Beware: ψk_out can lose information if the shift ΔG is large or if the G_vectors differ between k-points.
sourceDFTK.transfer_blochwave_kpt — Methodtransfer_blochwave_kpt(
ψk_in,
- basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
+ basis_in::PlaneWaveBasis,
kpt_in::Kpoint,
- basis_out::PlaneWaveBasis{T, VT} where VT<:Real,
+ basis_out::PlaneWaveBasis,
kpt_out::Kpoint
) -> Any
-
Transfer an array ψk defined on basisin $k$-point kptin to basisout $k$-point kptout.
sourceDFTK.transfer_density — Methodtransfer_density(
+
Transfer an array ψk defined on basisin $k$-point kptin to basisout $k$-point kptout.
sourceDFTK.transfer_density — Methodtransfer_density(
ρ_in,
basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
basis_out::PlaneWaveBasis{T, VT} where VT<:Real
) -> Any
-
Transfer density (in real space) between two basis sets.
This function is fast by transferring only the Fourier coefficients from the small basis to the big basis.
Note that this implies that for even-sized small FFT grids doing the transfer small -> big -> small is not an identity (as the small basis has an unmatched Fourier component and the identity $c_G = c_{-G}^\ast$ does not fully hold).
Note further that for the direction big -> small employing this function does not give the same answer as using first transfer_blochwave and then compute_density.
sourceDFTK.transfer_mapping — Methodtransfer_mapping(
+
Transfer density (in real space) between two basis sets.
This function is fast by transferring only the Fourier coefficients from the small basis to the big basis.
Note that this implies that for even-sized small FFT grids doing the transfer small -> big -> small is not an identity (as the small basis has an unmatched Fourier component and the identity $c_G = c_{-G}^\ast$ does not fully hold).
Note further that for the direction big -> small employing this function does not give the same answer as using first transfer_blochwave and then compute_density.
sourceDFTK.transfer_mapping — Methodtransfer_mapping(
basis_in::PlaneWaveBasis,
- basis_out::PlaneWaveBasis
-) -> Base.Iterators.Zip{Tuple{Array{CartesianIndices{3, Tuple{UnitRange{Int64}, UnitRange{Int64}, UnitRange{Int64}}}, 3}, Array{CartesianIndices{3, Tuple{UnitRange{Int64}, UnitRange{Int64}, UnitRange{Int64}}}, 3}}}
-
Compute the index mapping between the global grids of two bases. Returns an iterator of 8 pairs (block_in, block_out). Iterated over these pairs x_out_fourier[block_out, :] = x_in_fourier[block_in, :] does the transfer from the Fourier coefficients x_in_fourier (defined on basis_in) to x_out_fourier (defined on basis_out, equally provided as Fourier coefficients).
sourceDFTK.transfer_mapping — Methodtransfer_mapping(
- basis_in::PlaneWaveBasis{T, VT} where VT<:Real,
kpt_in::Kpoint,
- basis_out::PlaneWaveBasis{T, VT} where VT<:Real,
+ basis_out::PlaneWaveBasis,
kpt_out::Kpoint
) -> Tuple{Any, Any}
-
Compute the index mapping between two bases. Returns two arrays idcs_in and idcs_out such that ψkout[idcs_out] = ψkin[idcs_in] does the transfer from ψkin (defined on basis_in and kpt_in) to ψkout (defined on basis_out and kpt_out).
sourceDFTK.trapezoidal — Functiontrapezoidal(x, y)
Integrate y(x) over x using trapezoidal method quadrature.
sourceDFTK.unfold_bz — Methodunfold_bz(basis::PlaneWaveBasis) -> PlaneWaveBasis
-
" Convert a basis into one that doesn't use BZ symmetry. This is mainly useful for debug purposes (e.g. in cases we don't want to bother thinking about symmetries).
sourceDFTK.versioninfo — Functionversioninfo()
+
Compute the index mapping between two bases. Returns two arrays idcs_in and idcs_out such that ψkout[idcs_out] = ψkin[idcs_in] does the transfer from ψkin (defined on basis_in and kpt_in) to ψkout (defined on basis_out and kpt_out).
sourceDFTK.transfer_mapping — Methodtransfer_mapping(
+ basis_in::PlaneWaveBasis,
+ basis_out::PlaneWaveBasis
+) -> Base.Iterators.Zip{Tuple{Array{CartesianIndices{3, Tuple{UnitRange{Int64}, UnitRange{Int64}, UnitRange{Int64}}}, 3}, Array{CartesianIndices{3, Tuple{UnitRange{Int64}, UnitRange{Int64}, UnitRange{Int64}}}, 3}}}
+
Compute the index mapping between the global grids of two bases. Returns an iterator of 8 pairs (block_in, block_out). Iterated over these pairs x_out_fourier[block_out, :] = x_in_fourier[block_in, :] does the transfer from the Fourier coefficients x_in_fourier (defined on basis_in) to x_out_fourier (defined on basis_out, equally provided as Fourier coefficients).
sourceDFTK.trapezoidal — Functiontrapezoidal(x, y)
Integrate y(x) over x using trapezoidal method quadrature.
sourceDFTK.unfold_bz — Methodunfold_bz(basis::PlaneWaveBasis) -> PlaneWaveBasis
+
" Convert a basis into one that doesn't use BZ symmetry. This is mainly useful for debug purposes (e.g. in cases we don't want to bother thinking about symmetries).
sourceDFTK.versioninfo — Functionversioninfo()
versioninfo(io::IO)
-
DFTK.versioninfo([io::IO=stdout])
Summary of version and configuration of DFTK and its key dependencies.
sourceDFTK.weighted_ksum — Methodweighted_ksum(basis::PlaneWaveBasis, array) -> Any
-
Sum an array over kpoints, taking weights into account
sourceDFTK.write_w90_eig — Methodwrite_w90_eig(fileprefix::String, eigenvalues; n_bands)
-
Write the eigenvalues in a format readable by Wannier90.
sourceDFTK.write_w90_win — Methodwrite_w90_win(
+
DFTK.versioninfo([io::IO=stdout])
Summary of version and configuration of DFTK and its key dependencies.
sourceDFTK.weighted_ksum — Methodweighted_ksum(basis::PlaneWaveBasis, array) -> Any
+
Sum an array over kpoints, taking weights into account
sourceDFTK.write_w90_eig — Methodwrite_w90_eig(fileprefix::String, eigenvalues; n_bands)
+
Write the eigenvalues in a format readable by Wannier90.
sourceDFTK.write_w90_win — Methodwrite_w90_win(
fileprefix::String,
basis::PlaneWaveBasis;
bands_plot,
wannier_plot,
kwargs...
)
-
Write a win file at the indicated prefix. Parameters to Wannier90 can be added as kwargs: e.g. num_iter=500.
sourceDFTK.write_wannier90_files — Methodwrite_wannier90_files(
+
Write a win file at the indicated prefix. Parameters to Wannier90 can be added as kwargs: e.g. num_iter=500.
sourceDFTK.write_wannier90_files — Methodwrite_wannier90_files(
preprocess_call,
scfres;
n_bands,
@@ -965,15 +1016,15 @@
wannier_plot,
kwargs...
)
-
Shared file writing code for Wannier.jl and Wannier90.
sourceDFTK.ylm_real — Methodylm_real(
+
Shared file writing code for Wannier.jl and Wannier90.
sourceDFTK.ylm_real — Methodylm_real(
l::Integer,
m::Integer,
rvec::AbstractArray{T, 1}
) -> Any
-
Returns the (l,m) real spherical harmonic Ylm(r). Consistent with https://en.wikipedia.org/wiki/Tableofsphericalharmonics#Realsphericalharmonics
sourceDFTK.zeros_like — Functionzeros_like(X::AbstractArray) -> Any
+
Returns the (l,m) real spherical harmonic Ylm(r). Consistent with [wikipedia](https://en.wikipedia.org/wiki/Tableofsphericalharmonics#Realsphericalharmonics).
sourceDFTK.zeros_like — Functionzeros_like(X::AbstractArray) -> Any
zeros_like(
X::AbstractArray,
T::Type,
dims::Integer...
) -> Any
-
Create an array of same "array type" as X filled with zeros, minimizing the number of allocations. This unifies CPU and GPU code, as the output will always be on the same device as the input.
sourceDFTK.@timing — MacroShortened version of the @timeit macro from TimerOutputs, which writes to the DFTK timer.
sourceDFTK.Smearing.A — MethodA term in the Hermite delta expansion
sourceDFTK.Smearing.H — MethodStandard Hermite function using physicist's convention.
sourceDFTK.Smearing.entropy — MethodEntropy. Note that this is a function of the energy x, not of occupation(x). This function satisfies s' = x f' (see https://www.vasp.at/vasp-workshop/k-points.pdf p. 12 and https://arxiv.org/pdf/1805.07144.pdf p. 18.
sourceDFTK.Smearing.occupation — Functionoccupation(S::SmearingFunction, x)
Occupation at x, where in practice x = (ε - εF) / temperature. If temperature is zero, (ε-εF)/temperature = ±∞. The occupation function is required to give 1 and 0 respectively in these cases.
sourceDFTK.Smearing.occupation_derivative — MethodDerivative of the occupation function, approximation to minus the delta function.
sourceDFTK.Smearing.occupation_divided_difference — Method(f(x) - f(y))/(x - y), computed stably in the case where x and y are close
sourceSettings
This document was generated with Documenter.jl version 1.1.2 on Monday 25 December 2023. Using Julia version 1.9.4.
Create an array of same "array type" as X filled with zeros, minimizing the number of allocations. This unifies CPU and GPU code, as the output will always be on the same device as the input.
DFTK.@timing — MacroShortened version of the @timeit macro from TimerOutputs, which writes to the DFTK timer.
DFTK.Smearing.A — MethodA term in the Hermite delta expansion
DFTK.Smearing.H — MethodStandard Hermite function using physicist's convention.
DFTK.Smearing.entropy — MethodEntropy. Note that this is a function of the energy x, not of occupation(x). This function satisfies s' = x f' (see https://www.vasp.at/vasp-workshop/k-points.pdf p. 12 and https://arxiv.org/pdf/1805.07144.pdf p. 18.
DFTK.Smearing.occupation — Functionoccupation(S::SmearingFunction, x)Occupation at x, where in practice x = (ε - εF) / temperature. If temperature is zero, (ε-εF)/temperature = ±∞. The occupation function is required to give 1 and 0 respectively in these cases.
DFTK.Smearing.occupation_derivative — MethodDerivative of the occupation function, approximation to minus the delta function.
DFTK.Smearing.occupation_divided_difference — Method(f(x) - f(y))/(x - y), computed stably in the case where x and y are close
