Manual: The `Targets` Module

The Targets module implements the abstraction of targets and provides parameters of some commonly-used targets.

eTraj.Targets — Module

module Targets

The Targets module contains abstraction of the targets and provides some pre-defined atoms or molecules.

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eTraj.Targets.Target — Type

abstract type Target

Represents an abstract target, supertype of all targets.

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Manual: The Targets Module

Atoms under SAE approximation

The HydrogenLikeAtom and SAEAtom are both subtypes of the SAEAtomBase base type, which represents an atom under the SAE approximation. A key ingredient of atomic objects lies in the potential function of the residual ion after the electron gets ionized, which is the only difference between the two types.

The HydrogenLikeAtom's potential function is of the form:

\[\begin{equation} V(r) = -\frac{Z}{\sqrt{r^2+a}}, \end{equation}\]

with $a$ the soft-core parameter which avoids singularity of the potential during numerical simulation.

The SAEAtom's potential function is adopted from Tong's model ^[Tong_2005]:

\[\begin{equation} V(r) = -\frac{Z+a_1\ee^{-b_1 r}+a_2 r\ee^{-b_2 r}+a_3\ee^{-b_3 r}}{\sqrt{r^2+a}}, \end{equation}\]

where $a_i$ and $b_i$ are tunable parameters to fit the effective potential felt by the electron.

eTraj.Targets.SAEAtomBase — Type

abstract type SAEAtomBase <: Target

Represents an abstract atom under single-active-electron approximation.

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eTraj.Targets.HydrogenLikeAtom — Type

struct HydrogenLikeAtom <: SAEAtomBase <: Target

Represents a Hydrogen-like atom.

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eTraj.Targets.HydrogenLikeAtom — Method

HydrogenLikeAtom(Ip, Z [,l=0] [,m=0] [,asymp_coeff=:hartree|<coeff>] [,quan_ax_θ=0.0] [,quan_ax_ϕ=0.0] [,soft_core=1e-10] [,name]) <: SAEAtomBase

Initializes a new HydrogenLikeAtom.

Parameters

Ip : Ionization potential of the atom (numerically in a.u. or a Unitful.Quantity).
Z : Nuclear charge number.
l=0 : Angular quantum number (optional, default 0).
m=0 : Magnetic quantum number (optional, default 0).
asymp_coeff=:hartree : Asymptotic coefficient related to the wavefunction's behavior when r→∞ (:hartree or a positive number). Passing :hartree (by default) indicates automatic calculation using the Hartree formula.
quan_ax_θ=0.0 : Orientation angle θ of the quantization axis relative to the lab frame (numerically in radian or a Unitful.Quantity) (optional, default 0.0).
quan_ax_ϕ=0.0 : Orientation angle ϕ of the quantization axis relative to the lab frame (numerically in radian or a Unitful.Quantity) (optional, default 0.0).
soft_core=1e-10 : Soft core parameter of the Coulomb potential (optional, default 1e-10).
name::String : Name of the atom.

Examples

julia> t = HydrogenLikeAtom(Ip=0.5, Z=1, name="H")
[HydrogenLikeAtom] Atom H, Ip=0.5000 (13.61 eV), Z=1

julia> using eTraj.Units

julia> t = HydrogenLikeAtom(Ip=3.4eV, Z=1, l=1, name="H")
[HydrogenLikeAtom] Atom H (p orbital, m=0), Ip=0.1249 (3.40 eV), Z=1

See Also

The get_atom method provides some atom presets for use.

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eTraj.Targets.SAEAtom — Type

struct SAEAtom <: SAEAtomBase <: Targets

Represents an atom under single-active-electron (SAE) approximation.

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eTraj.Targets.SAEAtom — Method

SAEAtom(Ip, Z [,l=0] [,m=0] [,asymp_coeff=:hartree|<coeff>] [,quan_ax_θ=0.0] [,quan_ax_ϕ=0.0] [,a1,b1,a2,b2,a3,b3] [,soft_core=1e-10] [,name]) <: SAEAtomBase

Initializes a new SAEAtom.

Parameters

Ip : Ionization potential of the atom (numerically in a.u. or a Unitful.Quantity).
Z : Nuclear charge number.
l=0 : Angular quantum number (optional, default 0).
m=0 : Magnetic quantum number (optional, default 0).
asymp_coeff=:hartree: Asymptotic coefficient related to the wavefunction's behavior when r→∞ (:hartree or a positive number). Passing :hartree (by default) indicates automatic calculation using the Hartree formula.
quan_ax_θ=0.0 : Orientation angle θ of the quantization axis relative to the lab frame (numerically in radian or a Unitful.Quantity) (optional, default 0.0).
quan_ax_ϕ=0.0 : Orientation angle ϕ of the quantization axis relative to the lab frame (numerically in radian or a Unitful.Quantity) (optional, default 0.0).
a1,b1,a2,b2,a3,b3 : Parameters used to fit the atomic potential. See [J. Phys. B 38, 2593 (2005)]
soft_core=1e-10 : Soft core parameter to avoid singularity in the potential (optional, default 1e-10).
name::String : Name of the atom.

Examples

julia> t = SAEAtom(Ip=0.9035, Z=1, asymp_coeff=:hartree, a1=1.230723, b1=0.6620055, a2=-1.325040, b2=1.236224, a3=-0.2307230, b3=0.4804286, name="He")
[SAEAtom] Atom He, Ip=0.9035 (24.59 eV), Z=1

julia> using eTraj.Units

julia> t = SAEAtom(Ip=12.13eV, Z=1, l=1, a1=51.35554, b1=2.111554, a2=-99.92747, b2=3.737221, a3=1.644457, b3=0.4306465, asymp_coeff=1.3, name="Xe")
[SAEAtom] Atom Xe (p orbital, m=0), Ip=0.4458 (12.13 eV), Z=1

See Also

The get_atom method provides some atom presets for use.

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For the convenience of the user, there are some presets of commonly-used atoms, which can be accessed through the get_atom method. Available keys are accessed by invoking get_available_atoms.

HydrogenLikeAtom : H, He⁺, Li²⁺
SAEAtom : He, Ne, Ne⁺, Ne²⁺, Ar, Ar⁺, Ar²⁺, V, Ni, Kr, Kr⁺, Rb, Nb, Pd, Xe, Xe⁺, Ta

eTraj.Targets.get_atom — Function

get_atom(name::String, charge::Integer=0; kwargs...)

Constructs a HydrogenLikeAtom or SAEAtom in the database based on the name and charge given, other initialization parameters can be passed via kwargs. For HydrogenLikeAtom, the init params include Ip,Z and name; for SAEAtom, the init params include Ip,Z,a1,b1,a2,b2,a3,b3,l and name. The available keys can be found by invoking get_available_atoms.

Examples

julia> get_atom("H")
[HydrogenLikeAtom] Atom H, Ip=0.5000 (13.61 eV), Z=1

julia> get_atom("He")
[SAEAtom] Atom He, Ip=0.9036 (24.59 eV), Z=1

julia> get_atom("Ar"; m=1, asymp_coeff=0.950) # asymp_coeff from [Phys.-Uspekhi 47, 855 (2004)] (l=0 case)
[SAEAtom] Atom Ar (p orbital, m=1), Ip=0.5792 (15.76 eV), Z=1

julia> get_atom("Xe", 1)
[SAEAtom] Atom Xe⁺ (p orbital, m=0), Ip=0.7708 (20.97 eV), Z=2

julia> get_atom("Xe", 2)
ERROR: [get_atom] Atom name key `Xe2p` not found in database.
[...]

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eTraj.Targets.get_available_atoms — Function

Gets the available atom keys in the atom database, which are used to access atom objects using get_atom.

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Molecules

For molecule targets, the GenericMolecule type is implemented based on the MoleculeBase supertype, whose structure is more complicated. A GenericMolecule stores information about the atoms that make up the molecule, together with their coordinates, as well as the asymptotic coefficients [$C_{lm}$ in Eq. (38) in Molecular SFA] and WFAT's integral coefficients [Eq. (56) in WFAT], which are obtained using other quantum chemistry packages.

There are two ways to initialize a GenericMolecule: build from zero or from an existing file.

eTraj.Targets.MoleculeBase — Type

abstract type MoleculeBase <: Target

Represents an abstract molecule.

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eTraj.Targets.GenericMolecule — Type

struct GenericMolecule <: MoleculeBase <: Target

Represents a generic molecule.

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eTraj.Targets.GenericMolecule — Method

GenericMolecule(atoms, atom_coords [,charge=0] [,spin=0] [,name] [,rot_α=0.0] [,rot_β=0.0] [,rot_γ=0.0])

Initializes a new GenericMolecule with given parameters.

Parameters

atoms : Atoms in the molecule, stored as a Vector of String.
atom_coords : Atoms' coordinates in the molecule (numerically in Å or a Unitful.Quantity), stored as a N×3 Matrix.
charge : Total charge of the molecule (ion) (optional, default 0).
spin : Total spin of the molecule (optional, default 0). Note that each unpaired electron contributes 1/2.
name : Name of the molecule (optional).
rot_α,rot_β,rot_γ : Euler angles (z-y'-z'' convention) specifying the molecule's orientation (numerically in radian or a Unitful.Quantity) (optional, default 0).

Example

julia> m = GenericMolecule(atoms=["H","H"], atom_coords=[0.0 0.0 -0.375; 0.0 0.0 0.375], name="Hydrogen")
[GenericMolecule] Hydrogen

julia> using eTraj.Units

julia> m = GenericMolecule(atoms=["H","H"], atom_coords=[0.0 0.0 -0.375; 0.0 0.0 0.375]*Å, name="Hydrogen", rot_β=90°)
[GenericMolecule] Hydrogen, αβγ=(0.0°,90.0°,0.0°)

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eTraj.Targets.LoadMolecule — Function

LoadMolecule(ext_data_path; [rot_α=0.0] [,rot_β=0.0] [,rot_γ=0.0])

Initializes a new GenericMolecule with the data stored in ext_data_path.

Parameters

ext_data_path : Path to the molecule's data stored externally.
rot_α,rot_β,rot_γ : Euler angles (z-y'-z'' convention) specifying the molecule's orientation (numerically in radian or a Unitful.Quantity) (optional, default 0).

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We also provide some pre-defined molecules, which can be accessed through the get_mol method.

eTraj.Targets.get_mol — Function

get_mol(name::String; [rot_α=0.0] [,rot_β=0.0] [,rot_γ=0.0])

Constructs a GenericMolecule in the database based on the name given. Euler angles which describe the molecule's rotation can be applied via the keyword arguments rot_α, rot_β and rot_γ. The available molecule names can be found by invoking get_available_mols.

Examples


julia> get_mol("Hydrogen")
[GenericMolecule] Hydrogen (H₂)
Asymp coeff of HOMO available
WFAT data of HOMO available
#          E (Ha)  occp
⋮  ⋮         ⋮      ⋮⋮
3  LUMO+1   0.232  ----
2  LUMO     0.148  ----
1  HOMO    -0.594  -↿⇂-

julia> get_mol("Oxygen"; rot_β=π)
[GenericMolecule] Oxygen (O₂), αβγ=(0.0°,180.0°,0.0°)
Asymp coeff of α-HOMO-1 & α-HOMO available
WFAT data of α-HOMO-1 & α-HOMO available
#          Eα(Ha)  occp  Eβ(Ha)
⋮    ⋮        ⋮     ⋮⋮      ⋮     ⋮
11 LUMO+1   0.681  ----   0.741 LUMO+3
10 LUMO     0.377  ----   0.431 LUMO+2
9  HOMO    -0.554  -↿--   0.110 LUMO+1
8  HOMO-1  -0.554  -↿--   0.110 LUMO
7  HOMO-2  -0.763  -↿⇂-  -0.575 HOMO
6  HOMO-3  -0.841  -↿⇂-  -0.575 HOMO-1
5  HOMO-4  -0.841  -↿⇂-  -0.702 HOMO-2
4  HOMO-5  -1.204  -↿⇂-  -0.993 HOMO-3
⋮    ⋮        ⋮     ⋮⋮      ⋮     ⋮

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eTraj.Targets.get_available_mols — Function

Gets the available molecule keys in the molecule database, which are used to access molecule objects using get_mol.

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Molecule's Orientation

The molecule's orientation is described by a set of Euler angles ($z-y'-z''$ convention), which defines a rotational transformation from the molecular frame (MF) to the lab frame (LF). This property is NOT included in the saved file and thus needs to be specified each time upon initialization of the GenericMolecule object from external files.

Note

Here the three Euler angles (α,β,γ) that describe the GenericMolecule's orientation are completely different from that of the Euler angles (θ,χ) in the WFAT and MO-SFA theory. These theories' "lab frame" is chosen for convenience of theoretical formulation, where the electric field is assumed to be static, pointing towards the $+z$ direction, and has no relation with the lab frame mentioned above.

The orientation of the molecule can be obtained and set via the MolRotation and SetMolRotation! methods.

Quantum Chemistry Calculation

As for the quantum chemistry calculation, we implemented the scheme in PySCFMolecularCalculator using the PySCF, which works on Linux and macOS platforms (as a remedy, Windows users can use the Windows Subsystem of Linux (WSL)). The calculation scheme of WFAT structure factor is adopted from PyStructureFactor. Future extension is possible by implementing the supertype MolecularCalculatorBase. Since there are some presets of molecules available via get_mol, we are not going to detail on the manual of running the calculation in the text.

The example of initializing and calculating the essential data of GenericMolecule in REPL is presented as follows:

julia> using eTraj.Targets, eTraj.Units

julia> mol = GenericMolecule(atoms=["O","C","O"], atom_coords=[0 0 -1.1600; 0 0 0; 0 0 1.1600]*Å, charge=0, name="Carbon Dioxide (CO₂)")
[GenericMolecule] Carbon Dioxide (CO₂)

julia> MolInitCalculator!(mol, basis="cc-pVTZ")
[ Info: [PySCFMolecularCalculator] Running molecular calculation...

julia> MolCalcAsympCoeff!(mol, 0); MolCalcAsympCoeff!(mol, -1)
[ Info: [PySCFMolecularCalculator] Running calculation of asymptotic coefficients... (ionizing orbital HOMO)
[ Info: [PySCFMolecularCalculator] Running calculation of asymptotic coefficients... (ionizing orbital HOMO-1)

julia> MolCalcWFATData!(mol, 0); MolCalcWFATData!(mol, -1)
[ Info: [PySCFMolecularCalculator] Running calculation of WFAT structure factor data... (ionizing orbital HOMO)
[ Info: [PySCFMolecularCalculator] Running calculation of WFAT structure factor data... (ionizing orbital HOMO-1)

julia> MolSaveDataAs!(mol, "Molecule_CO2.jld2")
[ Info: [GenericMolecule] Data saved for molecule Carbon Dioxide (CO₂) at `Molecule_CO2.jld2`.

julia> mol_ = LoadMolecule("Molecule_CO2.jld2")  # load from saved file
[GenericMolecule] Carbon Dioxide (CO₂)
Asymp coeff of HOMO-1 & HOMO available
WFAT data of HOMO-1 & HOMO available
#          E (Ha)  occp
⋮    ⋮       ⋮      ⋮⋮
13 LUMO+1   0.207  ----
12 LUMO     0.175  ----
11 HOMO    -0.542  -↿⇂-
10 HOMO-1  -0.542  -↿⇂-
9  HOMO-2  -0.714  -↿⇂-
8  HOMO-3  -0.714  -↿⇂-
⋮    ⋮       ⋮      ⋮⋮

List of Available Properties & Methods

Generic `Target`

eTraj.Targets.IonPotential — Function

IonPotential(t::SAEAtomBase)

Gets the ionization potential of the atom.

IonPotential(mol::GenericMolecule)

Gets the ionization potential of the molecule's HOMO.

IonPotential(mol::GenericMolecule, orbit_ridx)

Gets the ionization potential of the specified MO of molecule.

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.AsympNuclCharge — Function

AsympNuclCharge(t::Target)

Gets the asymptotic nuclear charge of the target (after an electron got ionized).

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eTraj.Targets.TargetName — Function

TargetName(t::Target)

Gets the name of the target.

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eTraj.Targets.TargetPotential — Function

TargetPotential(t::SAEAtomBase) -> V(x,y,z)

Gets the potential function of the atom.

TargetPotential(mol::GenericMolecule) -> V(x,y,z)

Gets the asymptotic Coulomb potential function of the molecule.

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eTraj.Targets.TargetForce — Function

TargetForce(t::SAEAtomBase) -> F(x,y,z) -> (Fx,Fy,Fz)

Gets the Coulomb force exerted on the electron from the atom.

TargetForce(mol::GenericMolecule) -> F(x,y,z) -> (Fx,Fy,Fz)

Gets the asymptotic Coulomb force exerted on the electron from the molecular ion.

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eTraj.Targets.TrajectoryFunction — Function

TrajectoryFunction(t::Target, dimension = 2|3, laserFx::Function, laserFy::Function, phase_method = :CTMC|:QTMC|:SCTS)

Gets the trajectory function of the electron according to given parameter.

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`SAEAtomBase`

eTraj.Targets.AngularQuantumNumber — Function

AngularQuantumNumber(t::SAEAtomBase)

Gets the angular quantum number (l) of the atom.

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eTraj.Targets.MagneticQuantumNumber — Function

MagneticQuantumNumber(t::SAEAtomBase)

Gets the magnetic quantum number (m) of the atom.

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eTraj.Targets.AsympCoeff — Function

AsympCoeff(t::SAEAtomBase)

Gets the asymptotic coefficient (C_κl) of the atom.

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eTraj.Targets.SoftCore — Function

SoftCore(t::SAEAtomBase)

Gets the soft core parameter of the atom.

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eTraj.Targets.QuantizationAxisOrientaion — Function

QuantizationAxisOrientaion(t::SAEAtomBase)

Gets the orientation of the quantization axis of the atom in spherical coordinates (θ,ϕ).

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`GenericMolecule`

eTraj.Targets.MolAtoms — Function

MolAtoms(mol::GenericMolecule) -> ["atom1","atom2",...]

Gets the atoms in the molecule with their coordinates.

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eTraj.Targets.MolAtomCoords — Function

MolAtomCoords(mol::GenericMolecule) -> [x1 y1 z1; x2 y2 z2; ...]

Gets the atoms' coordinates in the molecule.

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eTraj.Targets.MolCharge — Function

MolCharge(mol::GenericMolecule)

Gets the total charge of the molecule.

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eTraj.Targets.MolSpin — Function

MolSpin(mol::GenericMolecule)

Gets the total spin of the molecule. Each unpaired electron contributes 1/2.

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eTraj.Targets.MolEnergyDataAvailable — Function

MolEnergyDataAvailable(mol::GenericMolecule)

Gets the availability of the energy data of the molecule.

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eTraj.Targets.MolEnergyLevels — Function

MolEnergyLevels(mol::GenericMolecule [,spin=1|2])

Gets the energy levels of the molecule's MOs.

spin: For closed-shell molecules, the spin param should be neglected. For open-shell molecules (with non-zero spins), spin=1 indicates α orbitals and spin=2 indicates β orbitals, neglecting spin would return both two sets of orbitals.

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eTraj.Targets.MolEnergyLevel — Function

MolEnergyLevel(mol::GenericMolecule, orbit_ridx)

Gets the energy level of the molecule's selected MO.

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.MolOrbitalOccupation — Function

MolOrbitalOccupation(mol::GenericMolecule [,spin=1|2])

Gets the occupation of the molecule's MOs.

spin: For closed-shell molecules, the spin param should be neglected. For open-shell molecules (with non-zero spins), spin=1 indicates α orbitals and spin=2 indicates β orbitals, neglecting spin would return both two sets of orbitals.

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eTraj.Targets.MolHOMOEnergy — Function

MolHOMOEnergy(mol::GenericMolecule [,spin=1|2])

Gets the energy of the molecule's HOMO.

spin: For closed-shell molecules, the spin param should be neglected. For open-shell molecules (with non-zero spins), spin=1 indicates α orbitals and spin=2 indicates β orbitals, neglecting spin would give both.

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eTraj.Targets.MolWFATAvailableIndices — Function

MolWFATAvailableIndices(mol::GenericMolecule)

Gets the available orbital indices (relative to HOMO) of the molecule's WFAT data.

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eTraj.Targets.MolWFATData — Function

MolWFATData(mol::GenericMolecule, orbit_ridx)

Gets the WFAT data in format (μ, int_data).

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.MolWFATStructureFactor_G — Function

MolWFATStructureFactor_G(mol::GenericMolecule, orbit_ridx, nξ, m, θ, χ)

Gets the WFAT structure factor $G_{n_ξ m}$ according to the given Euler angles θ and χ (z-y'-z'' convention). Note: the rotational Euler angles of the molecule would not be applied.

Parameters

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/θ spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.
nξ : Parabolic quantum number nξ=0,1,2,⋯ (nξ up to 5 is calculated by default).
m : Parabolic quantum number m=⋯,-1,0,1,⋯ (|m| up to 5 is calculated by default).
θ : Euler angle θ, passed as a Real value or an AbstractVector of Real.
χ : Euler angle χ, passed as a Real value or an AbstractVector of Real.

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eTraj.Targets.MolWFATMaxChannels — Function

MolWFATMaxChannels(mol::GenericMolecule, orbit_ridx)

Gets the maximum value of nξ and |m| calculated in the WFAT integral data.

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.MolAsympCoeffAvailableIndices — Function

MolAsympCoeffAvailableIndices(mol::GenericMolecule)

Gets the available orbital indices (relative to HOMO) of the molecule's asymptotic coefficients.

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eTraj.Targets.MolAsympCoeff — Function

MolAsympCoeff(mol::GenericMolecule, orbit_ridx)

Gets the asymptotic coefficients of the molecule.

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.MolAsympCoeff_lMax — Function

MolAsympCoeff_lMax(mol::GenericMolecule, orbit_ridx)

Gets the maximum value of l calculated in the asymptotic coefficients.

orbit_ridx: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.

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eTraj.Targets.MolRotation — Function

MolRotation(mol::GenericMolecule) -> (α,β,γ)

Gets the Euler angles (z-y'-z'' convention) specifying the molecule's orientation in format (α,β,γ) (in radian).

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eTraj.Targets.SetMolRotation! — Function

SetMolRotation!(mol::GenericMolecule, α,β,γ)
SetMolRotation!(mol::GenericMolecule, (α,β,γ))

Sets the Euler angles (z-y'-z'' convention) specifying the molecule's orientation in format (α,β,γ) (numerically in radian or a Unitful.Quantity).

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eTraj.Targets.MolExportAtomInfo — Function

MolExportAtomInfo(mol::GenericMolecule)

Exports the given molecule's atom information to string as MolecularCalculator's input.

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eTraj.Targets.MolInitCalculator! — Function

MolInitCalculator!(mol::GenericMolecule, MCType::Type=PySCFMolecularCalculator [;kwargs...])

Initializes the MolecularCalculator of mol with given parameters.

MCType : Type of MolecularCalculator if it is not initialized (default is PySCFMolecularCalculator).
kwargs... : Keyword arguments to pass to the initializer of MolecularCalculator of MCType, e.g., basis, ...

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eTraj.Targets.MolCalcWFATData! — Function

MolCalcWFATData!(mol::GenericMolecule [,orbit_ridx=0] [;kwargs...])

Calculates the WFAT data of the molecule.

orbit_ridx : Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.
kwargs... : Keyword arguments to pass to the calc_WFAT_data method, e.g. grid_rNum, grid_rMax, sf_lMax, ⋯

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eTraj.Targets.MolCalcAsympCoeff! — Function

MolCalcAsympCoeff!(mol::GenericMolecule, orbit_ridx; kwargs...)

Calculates the asymptotic coefficients of the molecule.

orbit_ridx : Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.
kwargs... : Keyword arguments to pass to the calc_asymp_coeff, e.g. grid_rNum, l_max.

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eTraj.Targets.MolSaveDataAs! — Function

MolSaveDataAs!(mol::GenericMolecule, data_path [,overwrite=false])

Saves the data of the GenericMolecule to the data_path. To overwrite the existing file, set overwrite=true.

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`MolecularCalculators`

eTraj.Targets.MolecularCalculatorBase — Type

abstract type MolecularCalculatorBase

Supertype of all molecular calculators.

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eTraj.Targets.PySCFMolecularCalculator — Type

struct PySCFMolecularCalculator <: MolecularCalculatorBase

An interface of molecular calculation using PySCF.

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eTraj.Targets.PySCFMolecularCalculator — Method

PySCFMolecularCalculator(; mol::MoleculeBase, basis::String="cc-pVDZ", kwargs...)

Initializes an instance of PySCFMolecularCalculator with given parameter.

Parameters

mol::MoleculeBase : The molecule to be calculated.
basis="cc-pVDZ" : Basis set used for calculation (default "cc-pVDZ").

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eTraj.Targets.calc_WFAT_data — Function

Calculates the data used in WFAT structure factor calculation of the given molecule.

Returns

(μ, int_data) : Orbital dipole momentum and the array which stores the integrals.

Parameters

mc : The molecular calculator.
orbit_ridx : Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.
grid_rNum : The number of radial grid (default 200).
grid_rMax : The maximum radius of the radial grid (default 10.0).
grid_θNum : The number of angular grid in the θ direction (default 60).
grid_ϕNum : The number of angular grid in the ϕ direction (default 60).
sf_nξMax : The maximum number of nξ used in calculation (default 3).
sf_mMax : The maximum number of |m| used in calculation (default 3).
sf_lMax : The maximum angular quantum number l used in calculation (default 6).
swap_HOMO_LUMO=false : If the HOMO & LUMO are degenerate, set swap_HOMO_LUMO=true when calculating LUMO (ridx=1). The program would swap the coefficients of HOMO and LUMO.

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eTraj.Targets.calc_asymp_coeff — Function

Calculates the asymptotic coefficients (used in ADK, SFA-SPANE, SFA-SPA) of the given molecule.

Parameters

mc : The molecular calculator.
orbit_ridx : Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO, and -1 indicates HOMO-1). For open-shell molecules, according to α/β spins, should be passed in format (spin, idx) where for α orbitals spin=1 and for β orbitals spin=2.
grid_rNum : The number of radial grid (default 200).
grid_rReg : The region of radial distance to fit the wavefunction to obtain the coefficients (default (3,8)).
grid_θNum : The number of angular grid in the θ direction (default 60).
grid_ϕNum : The number of angular grid in the ϕ direction (default 60).
l_max : The maximum number of l calculated (default 6).

source

Tong_2005X. M. Tong and C. D. Lin, Empirical formula for static field ionization rates of atoms and molecules by lasers in the barrier-suppression regime, J. Phys. B: At. Mol. Opt. Phys. 38, 2593 (2005). DOI: 10.1088/0953-4075/38/15/001