structures.layers

`structures.layers`#

Classes:

`Layer`(id, name, **kwargs)	Base class of real physical layers, such as amorphous layers and unit cells.
`AmorphousLayer`(id, name, thickness, density, ...)	Representation of amorphous layers containing an Atom or AtomMixed.
`UnitCell`(id, name, c_axis, **kwargs)	Representation of unit cells made of one or multiple Atom or AtomMixed instances at defined positions.

class udkm1Dsim.structures.layers.Layer(id, name, **kwargs)[source]#

Bases: object

Base class of real physical layers, such as amorphous layers and unit cells.

It holds different structural, thermal, and elastic properties that are relevant for simulations.

Parameters:

id (str) – id of the layer.
name (str) – name of the layer.

Keyword Arguments:

roughness (float) – gaussian width of the top roughness of a layer.
deb_wal_fac (float) – Debye Waller factor.
sound_vel (float) – sound velocity.
phonon_damping (float) – phonon damping.
opt_pen_depth (float) – optical penetration depth.
opt_ref_index (float) – refractive index.
opt_ref_index_per_strain (float) – change of refractive index per strain.
heat_capacity (float) – heat capacity.
therm_cond (float) – thermal conductivity.
lin_therm_exp (float) – linear thermal expansion.
sub_system_coupling (float) – sub-system coupling.

Attributes:

id (str) – id of the layer.
name (str) – name of the layer.
thickness (float) – thickness of the layer [m].
mass (float) – mass of the layer [kg].
mass_unit_area (float) – mass of layer normalized to unit area of 1 Å² [kg].
density (float) – density of the layer [kg/m³].
area (float) – area of layer [m²].
volume (float) – volume of layer [m³].
roughness (float) – gaussian width of the top roughness of a layer [m].
deb_wal_fac (float) – Debye-Waller factor [m²].
sound_vel (float) – longitudinal sound velocity in the layer [m/s].
spring_const (ndarray[float]) – spring constant of the layer [kg/s²] and higher orders.
phonon_damping (float) – damping constant of phonon propagation [kg/s].
opt_pen_depth (float) – optical penetration depth of the layer [m].
opt_ref_index (ndarray[float]) – optical refractive index - real and imagenary part \(n + i\kappa\).
opt_ref_index_per_strain (ndarray[float]) – optical refractive index change per strain - real and imagenary part \(\frac{d n}{d \eta} + i\frac{d \kappa}{d \eta}\).
therm_cond (list[@lambda]) – list of T-dependent thermal conductivity [W/(m K)].
lin_therm_exp (list[@lambda]) – list of T-dependent linear thermal expansion coefficient (relative).
int_lin_therm_exp (list[@lambda]) – list of T-dependent integrated linear thermal expansion coefficient.
heat_capacity (list[@lambda]) – list of T-dependent heat capacity function [J/(kg K)].
int_heat_capacity (list[@lambda]) – list of T-dependent integrated heat capacity function.
sub_system_coupling (list[@lambda]) – list of coupling functions of different subsystems [W/m³].
num_sub_systems (int) – number of subsystems for heat and phonons (electrons, lattice, spins, …).
eff_spin (float) – effective spin.
curie_temp (float) – Curie temperature [K].
mf_exch_coupling (float) – mean field exchange coupling constant [m²kg/s²].
lamda (float) – intrinsic coupling to bath parameter.
mag_moment (float) – atomic magnetic moment [mu_Bohr].
aniso_exponent (ndarray[float]) – exponent of T-dependence uniaxial anisotropy.
anisotropy (float) – anisotropy at T=0 K [J/m³] as x,y,z component vector.
exch_stiffness (float) – exchange stiffness at T=0 K [J/m].
mag_saturation (float) – saturation magnetization at 0 K [J/T/m³].

Methods:

`check_input`(inputs)	Checks the input and create a list of function handle strings with T as argument.
`get_property_dict`(**kwargs)	Returns a dictionary with all parameters.
`get_acoustic_impedance`()	Calculates the acoustic impedance.
`set_ho_spring_constants`(HO)	Set the higher orders of the spring constant for anharmonic phonon simulations.
`set_opt_pen_depth_from_ref_index`(wavelength)	Set the optical penetration depth from the optical referactive index for a given wavelength.
`calc_spring_const`()	Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness
`calc_mf_exchange_coupling`()	Calculate the mean-field exchange coupling constant

check_input(inputs)[source]#

Checks the input and create a list of function handle strings with T as argument. Inputs can be strings, floats, ints, or pint quantaties.

Parameters:

inputs (list[str, int, float, Quantity]) – list of strings, int, floats, or Pint quantities.

Returns:

(tuple) –

output (list[@lambda]) - list of lambda functions.
output_strs (list[str]) - list of string-representations.

get_property_dict(**kwargs)[source]#

Returns a dictionary with all parameters. objects or dicts and objects are converted to strings. if a type is given, only these properties are returned.

Parameters:: **kwargs (list[str]) – types of requested properties.
Returns:: R (dict) – dictionary with requested properties.

get_acoustic_impedance()[source]#

Calculates the acoustic impedance.

Returns:: Z (float) – acoustic impedance.

set_ho_spring_constants(HO)[source]#

Set the higher orders of the spring constant for anharmonic phonon simulations.

Parameters:: HO (ndarray[float]) – higher order spring constants.

set_opt_pen_depth_from_ref_index(wavelength)[source]#

Set the optical penetration depth from the optical referactive index for a given wavelength.

Parameters:: wavelength (Quantity) – wavelength as Pint Quantitiy.

calc_spring_const()[source]#: Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness

\[k = m \, \left(\frac{v}{c}\right)^2\]

calc_mf_exchange_coupling()[source]#: Calculate the mean-field exchange coupling constant

\[J = \frac{3}{S_{eff}+1} k_B T_C\]

class udkm1Dsim.structures.layers.AmorphousLayer(id, name, thickness, density, **kwargs)[source]#

Bases: Layer

Representation of amorphous layers containing an Atom or AtomMixed.

Parameters:

id (str) – id of the layer.
name (str) – name of layer.
thickness (float) – thickness of the layer.
density (float) – density of the layer.

Keyword Arguments:

atom (object) – Atom or AtomMixed in the layer.
roughness (float) – gaussian width of the top roughness of a layer.
deb_wal_fac (float) – Debye Waller factor.
sound_vel (float) – sound velocity.
phonon_damping (float) – phonon damping.
roughness – gaussian width of the top roughness of a layer.
opt_pen_depth (float) – optical penetration depth.
opt_ref_index (float) – refractive index.
opt_ref_index_per_strain (float) – change of refractive index per strain.
heat_capacity (float) – heat capacity.
therm_cond (float) – thermal conductivity.
lin_therm_exp (float) – linear thermal expansion.
sub_system_coupling (float) – sub-system coupling.

Attributes:

id (str) – id of the layer.
name (str) – name of the layer.
thickness (float) – thickness of the layer [m].
mass (float) – mass of the layer [kg].
mass_unit_area (float) – mass of layer normalized to unit area of 1 Å² [kg].
density (float) – density of the layer [kg/m³].
area (float) – area of layer [m²].
volume (float) – volume of layer [m³].
roughness (float) – gaussian width of the top roughness of a layer [m].
deb_wal_fac (float) – Debye-Waller factor [m²].
sound_vel (float) – longitudinal sound velocity in the layer [m/s].
spring_const (ndarray[float]) – spring constant of the layer [kg/s²] and higher orders.
phonon_damping (float) – damping constant of phonon propagation [kg/s].
opt_pen_depth (float) – optical penetration depth of the layer [m].
opt_ref_index (ndarray[float]) – optical refractive index - real and imagenary part \(n + i\kappa\).
opt_ref_index_per_strain (ndarray[float]) – optical refractive index change per strain - real and imagenary part \(\frac{d n}{d \eta} + i\frac{d \kappa}{d \eta}\).
therm_cond (list[@lambda]) – list of HANDLES T-dependent thermal conductivity [W/(m K)].
lin_therm_exp (list[@lambda]) – list of T-dependent linear thermal expansion coefficient (relative).
int_lin_therm_exp (list[@lambda]) – list of T-dependent integrated linear thermal expansion coefficient.
heat_capacity (list[@lambda]) – list of T-dependent heat capacity function [J/(kg K)].
int_heat_capacity (list[@lambda]) – list of T-dependent integrated heat capacity function.
sub_system_coupling (list[@lambda]) – list of of coupling functions of different subsystems [W/m³].
num_sub_systems (int) – number of subsystems for heat and phonons (electrons, lattice, spins, …).
eff_spin (float) – effective spin.
curie_temp (float) – Curie temperature [K].
mf_exch_coupling (float) – mean field exchange coupling constant [m²kg/s²].
lamda (float) – intrinsic coupling to bath parameter.
mag_moment (float) – atomic magnetic moment [mu_Bohr].
aniso_exponent (ndarray[float]) – exponent of T-dependence uniaxial anisotropy.
anisotropy (float) – anisotropy at T=0 K [J/m³] as x,y,z component vector.
exch_stiffness (float) – exchange stiffness at T=0 K [J/m].
mag_saturation (float) – saturation magnetization at 0 K [J/T/m³].
magnetization (dict[float]) – magnetization amplitude, phi and gamma angle inherited from the atom.
atom (object) – Atom or AtomMixed in the layer.

Methods:

`calc_mf_exchange_coupling`()	Calculate the mean-field exchange coupling constant
`calc_spring_const`()	Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness
`check_input`(inputs)	Checks the input and create a list of function handle strings with T as argument.
`get_acoustic_impedance`()	Calculates the acoustic impedance.
`get_property_dict`(**kwargs)	Returns a dictionary with all parameters.
`set_ho_spring_constants`(HO)	Set the higher orders of the spring constant for anharmonic phonon simulations.
`set_opt_pen_depth_from_ref_index`(wavelength)	Set the optical penetration depth from the optical referactive index for a given wavelength.

calc_mf_exchange_coupling()#: Calculate the mean-field exchange coupling constant

\[J = \frac{3}{S_{eff}+1} k_B T_C\]

calc_spring_const()#: Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness

\[k = m \, \left(\frac{v}{c}\right)^2\]

check_input(inputs)#

Checks the input and create a list of function handle strings with T as argument. Inputs can be strings, floats, ints, or pint quantaties.

Parameters:

inputs (list[str, int, float, Quantity]) – list of strings, int, floats, or Pint quantities.

Returns:

(tuple) –

output (list[@lambda]) - list of lambda functions.
output_strs (list[str]) - list of string-representations.

get_acoustic_impedance()#

Calculates the acoustic impedance.

Returns:: Z (float) – acoustic impedance.

get_property_dict(**kwargs)#

Returns a dictionary with all parameters. objects or dicts and objects are converted to strings. if a type is given, only these properties are returned.

Parameters:: **kwargs (list[str]) – types of requested properties.
Returns:: R (dict) – dictionary with requested properties.

set_ho_spring_constants(HO)#

Set the higher orders of the spring constant for anharmonic phonon simulations.

Parameters:: HO (ndarray[float]) – higher order spring constants.

set_opt_pen_depth_from_ref_index(wavelength)#

Set the optical penetration depth from the optical referactive index for a given wavelength.

Parameters:: wavelength (Quantity) – wavelength as Pint Quantitiy.

class udkm1Dsim.structures.layers.UnitCell(id, name, c_axis, **kwargs)[source]#

Bases: Layer

Representation of unit cells made of one or multiple Atom or AtomMixed instances at defined positions.

Parameters:

id (str) – id of the UnitCell.
name (str) – name of the UnitCell.
c_axis (float) – c-axis of the UnitCell.

Keyword Arguments:

a_axis (float) – a-axis of the UnitCell.
b_axis (float) – b-axis of the UnitCell.
deb_wal_fac (float) – Debye Waller factor.
sound_vel (float) – sound velocity.
phonon_damping (float) – phonon damping.
roughness (float) – gaussian width of the top roughness of a layer.
opt_pen_depth (float) – optical penetration depth.
opt_ref_index (float) – refractive index.
opt_ref_index_per_strain (float) – change of refractive index per strain.
heat_capacity (float) – heat capacity.
therm_cond (float) – thermal conductivity.
lin_therm_exp (float) – linear thermal expansion.
sub_system_coupling (float) – sub-system coupling.

Attributes:

id (str) – id of the layer.
name (str) – name of the layer.
c_axis (float) – out-of-plane c-axis [m].
a_axis (float) – in-plane a-axis [m].
b_axis (float) – in-plane b-axis [m].
thickness (float) – thickness of the layer [m].
mass (float) – mass of the layer [kg].
mass_unit_area (float) – mass of layer normalized to unit area of 1 Å² [kg].
density (float) – density of the layer [kg/m³].
area (float) – area of layer [m²].
volume (float) – volume of layer [m³].
roughness (float) – gaussian width of the top roughness of a layer [m].
deb_wal_fac (float) – Debye-Waller factor [m²].
sound_vel (float) – longitudinal sound velocity in the layer [m/s].
spring_const (ndarray[float]) – spring constant of the layer [kg/s²] and higher orders.
phonon_damping (float) – damping constant of phonon propagation [kg/s].
opt_pen_depth (float) – optical penetration depth of the layer [m].
opt_ref_index (ndarray[float]) – optical refractive index - real and imagenary part \(n + i\kappa\).
opt_ref_index_per_strain (ndarray[float]) – optical refractive index change per strain - real and imagenary part \(\frac{d n}{d \eta} + i\frac{d \kappa}{d \eta}\).
therm_cond (list[@lambda]) – list of HANDLES T-dependent thermal conductivity [W/(m K)].
lin_therm_exp (list[@lambda]) – list of T-dependent linear thermal expansion coefficient (relative).
int_lin_therm_exp (list[@lambda]) – list of T-dependent integrated linear thermal expansion coefficient.
heat_capacity (list[@lambda]) – list of T-dependent heat capacity function [J/(kg K)].
int_heat_capacity (list[@lambda]) – list of T-dependent integrated heat capacity function.
sub_system_coupling (list[@lambda]) – list of of coupling functions of different subsystems [W/m³].
num_sub_systems (int) – number of subsystems for heat and phonons (electrons, lattice, spins, …).
atoms (list[atom, @lambda]) – list of atoms and function handle for strain dependent displacement.
num_atoms (int) – number of atoms in unit cell.
eff_spin (float) – effective spin.
curie_temp (float) – Curie temperature [K].
mf_exch_coupling (float) – mean field exchange coupling constant [m²kg/s²].
lamda (float) – intrinsic coupling to bath parameter.
mag_moment (float) – atomic magnetic moment [mu_Bohr].
aniso_exponent (ndarray[float]) – exponent of T-dependence uniaxial anisotropy.
anisotropy (float) – anisotropy at T=0 K [J/m³] as x,y,z component vector.
exch_stiffness (float) – exchange stiffness at T=0 K [J/m].
mag_saturation (float) – saturation magnetization at 0 K [J/T/m³].
magnetization (list[float]) – magnetization amplitudes, phi, and gamma angle of each atom in the unit cell.

Methods:

`calc_mf_exchange_coupling`()	Calculate the mean-field exchange coupling constant
`calc_spring_const`()	Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness
`check_input`(inputs)	Checks the input and create a list of function handle strings with T as argument.
`get_acoustic_impedance`()	Calculates the acoustic impedance.
`get_property_dict`(**kwargs)	Returns a dictionary with all parameters.
`set_ho_spring_constants`(HO)	Set the higher orders of the spring constant for anharmonic phonon simulations.
`set_opt_pen_depth_from_ref_index`(wavelength)	Set the optical penetration depth from the optical referactive index for a given wavelength.
`visualize`(**kwargs)	Allows for 3D presentation of unit cell by allow for a & b coordinate of atoms.
`add_atom`(atom, position)	Adds an AtomBase/AtomMixed at a relative position of the unit cell.
`add_multiple_atoms`(atom, position, Nb)	Adds multiple AtomBase/AtomMixed at a relative position of the unit cell.
`get_atom_ids`()	Provides a list of atom ids within the unit cell.
`get_atom_positions`(*args)	Calculates the relative positions of the atoms in the unit cell

calc_mf_exchange_coupling()#: Calculate the mean-field exchange coupling constant

\[J = \frac{3}{S_{eff}+1} k_B T_C\]

calc_spring_const()#: Calculates the spring constant of the layer from the mass per unit area, sound velocity and thickness

\[k = m \, \left(\frac{v}{c}\right)^2\]

check_input(inputs)#

Checks the input and create a list of function handle strings with T as argument. Inputs can be strings, floats, ints, or pint quantaties.

Parameters:

inputs (list[str, int, float, Quantity]) – list of strings, int, floats, or Pint quantities.

Returns:

(tuple) –

output (list[@lambda]) - list of lambda functions.
output_strs (list[str]) - list of string-representations.

get_acoustic_impedance()#

Calculates the acoustic impedance.

Returns:: Z (float) – acoustic impedance.

get_property_dict(**kwargs)#

Returns a dictionary with all parameters. objects or dicts and objects are converted to strings. if a type is given, only these properties are returned.

Parameters:: **kwargs (list[str]) – types of requested properties.
Returns:: R (dict) – dictionary with requested properties.

set_ho_spring_constants(HO)#

Set the higher orders of the spring constant for anharmonic phonon simulations.

Parameters:: HO (ndarray[float]) – higher order spring constants.

set_opt_pen_depth_from_ref_index(wavelength)#

Set the optical penetration depth from the optical referactive index for a given wavelength.

Parameters:: wavelength (Quantity) – wavelength as Pint Quantitiy.

visualize(**kwargs)[source]#

Allows for 3D presentation of unit cell by allow for a & b coordinate of atoms. Also add magnetization per atom.

Todo

use the avogadro project as plugin

Todo

create unit cell from CIF file e.g. by xrayutilities plugin.

Parameters:: **kwargs (str) – strain or magnetization for manipulating unit cell visualization.

add_atom(atom, position)[source]#

Adds an AtomBase/AtomMixed at a relative position of the unit cell.

Sort the list of atoms by the position at zero strain.

Update the mass, density and spring constant of the unit cell automatically:

\[\kappa = m \cdot (v_s / c)^2\]

Parameters:

atom (Atom, AtomMixed) – Atom or AtomMixed added to unit cell.
position (float) – relative position within unit cel [0 .. 1].

add_multiple_atoms(atom, position, Nb)[source]#

Adds multiple AtomBase/AtomMixed at a relative position of the unit cell.

Parameters:

atom (Atom, AtomMixed) – Atom or AtomMixed added to unit cell.
position (float) – relative position within unit cel [0 .. 1].
Nb (int) – repetition of atoms.

get_atom_ids()[source]#

Provides a list of atom ids within the unit cell.

Returns:: ids (list[str]) – list of atom ids within unit cell

get_atom_positions(*args)[source]#

Calculates the relative positions of the atoms in the unit cell

Returns:: res (ndarray[float]) – relative postion of the atoms within the unit cell.

structures.layers

Contents

structures.layers#

`structures.layers`#