Dislocation

matscipy.dislocation.make_screw_cyl(alat, C11, C12, C44, cylinder_r=10, cutoff=5.5, hard_core=False, center=[0.0, 0.0, 0.0], l_extend=[0.0, 0.0, 0.0], symbol='W')

Makes screw dislocation using atomman library

Parameters:

• alat (float) – Lattice constant of the material.

• C11 (float) – C11 elastic constant of the material.

• C12 (float) – C12 elastic constant of the material.

• C44 (float) – C44 elastic constant of the material.

• cylinder_r (float) – radius of cylinder of unconstrained atoms around the dislocation in angstrom

• cutoff (float) – Potential cutoff for Marinica potentials for FS cutoff = 4.4

• hard_core (bool) – Description of parameter hard_core.

• center (type) –

  The position of the dislocation core and the center of the

  cylinder with FixAtoms condition

• l_extend (float) – extension of the box. used for creation of initial dislocation position with box equivalent to the final position

• symbol (string) – Symbol of the element to pass to ase.lattice.cubic.SimpleCubicFactory default is “W” for tungsten

Returns:

• disloc (ase.Atoms object) – screw dislocation cylinder.

• bulk (ase.Atoms object) – bulk disk used to generate dislocation

• u (np.array) – displacement per atom.

matscipy.dislocation.make_edge_cyl(alat, C11, C12, C44, cylinder_r=10, cutoff=5.5, symbol='W')

makes edge dislocation using atomman library

cylinder_r - radius of cylinder of unconstrained atoms around the

dislocation in angstrom

cutoff - potential cutoff for Marinica potentials for FS cutoff = 4.4

symbolstring

Symbol of the element to pass to ase.lattice.cubic.SimpleCubicFactory default is “W” for tungsten

matscipy.dislocation.plot_vitek(dislo, bulk, alat=3.16, plot_axes=None, xyscale=10)

Plots vitek map from ase configurations.

Parameters:

• dislo (ase.Atoms) – Dislocation configuration.

• bulk (ase.Atoms) – Corresponding bulk configuration for calculation of displacements.

• alat (float) – Lattice parameter for calculation of neighbour list cutoff.

• plot_axes (matplotlib.Axes.axes object) – Existing axes to plot on, allows to pass existing matplotlib axes have full control of the graph outside the function. Makes possible to plot multiple differential displacement maps using subplots. Default is None, then new graph is created by plt.subplots() Description of parameter plot_axes.

• xyscale (float) – xyscale of the graph

Return type:

None

matscipy.dislocation.show_NEB_configurations(images, bulk, xyscale=7, show=True, core_positions=None)

Plots Vitek differential displacement maps for the list of images

for example along the NEB path.

Parameters:

• images (list of ase.Atoms) – List of configurations with dislocations.

• bulk (ase.Atoms) – Corresponding bulk configuration for calculation of displacements.

• xyscale (float) – xyscale of the graph

• show (bool) – Show the figure after plotting. Default is True.

• core_positions (list) – [x, y] position of dislocation core to plot

Returns:

If the show is False else returns None

Return type:

figure

matscipy.dislocation.show_configuration(disloc, bulk, u, fixed_mask=None)

shows the displacement fixed atoms.

matscipy.dislocation.get_elastic_constants(pot_path=None, calculator=None, delta=0.01, symbol='W')

return lattice parameter, and cubic elastic constants: C11, C12, 44 using matscipy function pot_path - path to the potential

symbolstring

Symbol of the element to pass to ase.lattice.cubic.SimpleCubicFactory default is “W” for tungsten

matscipy.dislocation.make_barrier_configurations(elastic_param=None, pot_path=None, calculator=None, cylinder_r=10, hard_core=False, **kwargs)

Creates the initial and final configurations for the NEB calculation

The positions in FixedAtoms constrained region are average between final and initial configurations

Parameters:

• pot_path (string) – Path to the potential file.

• calculator (type) – Description of parameter calculator.

• cylinder_r (float) –

  Radius of cylinder of unconstrained atoms around the

  dislocation in angstrom.

• hard_core (bool) – Type of the core hard or soft. If hard is chosen the displacement field is reversed.

• **kwargs – Keyword arguments to pass to make_screw_cyl() function.

Returns:

• disloc_ini (ase.Atoms) – Initial dislocation configuration.

• disloc_fin (ase.Atoms) – Final dislocation configuration.

• bulk (ase.Atoms) – Perfect bulk configuration for Vitek displacement maps

matscipy.dislocation.make_screw_cyl_kink(alat, C11, C12, C44, cylinder_r=40, kink_length=26, kind='double', **kwargs)

Function to create kink configuration based on make_screw_cyl() function. Double kink configuration is in agreement with quadrupoles in terms of formation energy. Single kink configurations provide correct and stable structure, but formation energy is not accessible?

Parameters:

• alat (float) – Lattice constant of the material.

• C11 (float) – C11 elastic constant of the material.

• C12 (float) – C12 elastic constant of the material.

• C44 (float) – C44 elastic constant of the material.

• cylinder_r (float) – radius of cylinder of unconstrained atoms around the dislocation in angstrom

• kink_length (int) – Length of the cell per kink along b in unit of b, must be even.

• kind (string) – kind of the kink: right, left or double

• **kwargs – Keyword arguments to pass to make_screw_cyl() function.

Returns:

• kink (ase.atoms) – kink configuration

• reference_straight_disloc (ase.atoms) – reference straight dislocation configuration

• large_bulk (ase.atoms) – large bulk cell corresponding to the kink configuration

matscipy.dislocation.slice_long_dislo(kink, kink_bulk, b)

Function to slice a long dislocation configuration to perform

dislocation structure and core position analysis

Parameters:

• kink (ase.Atoms) – kink configuration to slice

• kink_bulk (ase.Atoms) – corresponding bulk configuration to perform mapping for slicing

• b (float) – burgers vector b should be along z direction

Returns:

• sliced_kink (list of [sliced_bulk, sliced_kink]) – sliced configurations 1 b length each

• disloc_z_positions (float) – positions of each sliced configuration (center along z)

matscipy.dislocation.compare_configurations(dislo, bulk, dislo_ref, bulk_ref, alat, cylinder_r=None, print_info=True, remap=True, bulk_neighbours=None, origin=(0.0, 0.0))

Compares two dislocation configurations based on the gradient of

the displacements along the bonds.

Parameters:

• dislo (ase.Atoms) – Dislocation configuration.

• bulk (ase.Atoms) – Corresponding bulk configuration for calculation of displacements.

• dislo_ref (ase.Atoms) – Reference dislocation configuration.

• bulk_ref (ase.Atoms) – Corresponding reference bulk configuration for calculation of displacements.

• alat (float) – Lattice parameter for calculation of neghbour list cutoff.

• cylinder_r (float or None) – Radius of region of comparison around the dislocation coreself. If None makes global comparison based on the radius of dislo configuration, else compares the regions with cylinder_r around the dislocation core position.

• print_info (bool) – Flag to switch print statement about the type of the comparison

• remap (bool) – Flag to swtich off remapping of atoms between deformed and reference configurations. Only set this to true if atom order is the same!

• bulk_neighbours – Optionally pass in bulk neighbours as a tuple (bulk_i, bulk_j)

• origin (tuple) – Optionally pass in coordinate origin (x0, y0)

Returns:

The Du norm of the differences per atom.

Return type:

float

matscipy.dislocation.cost_function(pos, dislo, bulk, cylinder_r, elastic_param, hard_core=False, print_info=True, remap=True, bulk_neighbours=None, origin=(0, 0))

Cost function for fitting analytical displacement field

and detecting dislocation core position. Uses compare_configurations function for the minimisation of the core position.

Parameters:

• pos (list of float) – Positions of the core to build the analytical solution [x, y].

• dislo (ase.Atoms) – Dislocation configuration.

• bulk (ase.Atoms) – Corresponding bulk configuration for calculation of displacements.

• cylinder_r (float or None) – Radius of region of comparison around the dislocation coreself. If None makes global comparison based on the radius of dislo configuration, else compares the regions with cylinder_r around the dislocation core position.

• elastic_param (list of float) – List containing alat, C11, C12, C44

• hard_core (bool) – type of the core True for hard

• print_info (bool) – Flag to switch print statement about the type of the comparison

• bulk_neighbours (tuple or None) – Optionally pass in neighbour list for bulk reference config to save computing it each time.

• origin (tuple) – Optionally pass in coordinate origin (x0, y0)

Returns:

Error for optimisation (result from compare_configurations function)

Return type:

float

matscipy.dislocation.fit_core_position(dislo_image, bulk, elastic_param, hard_core=False, core_radius=10, current_pos=None, bulk_neighbours=None, origin=(0, 0))

Use cost_function() to fit atomic positions to Stroh solution with

scipy.optimize.minimize is used to perform the fit using Powell’s method.

Parameters:

• dislo_image (ase.atoms.Atoms) –

• bulk (ase.atoms.Atoms) –

• elastic_param (array-like) – [alat, C11, C12, C44]

• hard_core (bool) –

• core_radius (float) –

• current_pos (array-like) – array [core_x, core_y] containing initial guess for core position

• bulk_neighbours (tuple) – cache of bulk neigbbours to speed up calcualtion. Should be a tuple (bulk_I, bulk_J) as returned by matscipy.neigbbours.neighbour_list(‘ij’, bulk, alat).

• origin (tuple) – Optionally pass in coordinate origin (x0, y0)

Return type:

core_pos - array [core_x, core_y]

matscipy.dislocation.fit_core_position_images(images, bulk, elastic_param, bulk_neighbours=None, origin=(0, 0))

Call fit_core_position() for a list of Atoms objects, e.g. NEB images

Parameters:

• images (list) – list of Atoms object for dislocation configurations

• bulk (ase.atoms.Atoms) – bulk reference configuration

• elastic_param (list) – as for fit_core_position().

• bulk_neighbours – as for fit_core_position().

• origin (tuple) – Optionally pass in coordinate origin (x0, y0)

Returns:

core_positions

Return type:

array of shape (len(images), 2)

matscipy.dislocation.screw_cyl_tetrahedral(alat, C11, C12, C44, scan_r=15, symbol='W', imp_symbol='H', hard_core=False, center=(0.0, 0.0, 0.0))

Generates a set of tetrahedral positions with scan_r radius.

Applies the screw dislocation displacement for creating an initial guess for the H positions at dislocation core.

Parameters:

• alat (float) – Lattice constant of the material.

• C11 (float) – C11 elastic constant of the material.

• C12 (float) – C12 elastic constant of the material.

• C44 (float) – C44 elastic constant of the material.

• scan_r (float) – Radius of the region to create tetrahedral positions.

• symbol (string) – Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory default is “W” for tungsten

• imp_symbol (string) – Symbol of the elemnt to pass creat Atoms object default is “H” for hydrogen

• hard_core (float) – Type of the dislocatino core if True then -u (sign of displacement is flipped) is applied. Default is False i.e. soft core is created.

centertuple of floats

Coordinates of dislocation core (center) (x, y, z). Default is (0., 0., 0.)

Returns:

Atoms object with predicted tetrahedral positions around dislocation core.

Return type:

ase.Atoms object

matscipy.dislocation.screw_cyl_octahedral(alat, C11, C12, C44, scan_r=15, symbol='W', imp_symbol='H', hard_core=False, center=(0.0, 0.0, 0.0))

Generates a set of octahedral positions with scan_r radius.

Applies the screw dislocation displacement for creating an initial guess for the H positions at dislocation core.

Parameters:

• alat (float) – Lattice constant of the material.

• C11 (float) – C11 elastic constant of the material.

• C12 (float) – C12 elastic constant of the material.

• C44 (float) – C44 elastic constant of the material.

• symbol (string) – Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory default is “W” for tungsten

• imp_symbol (string) – Symbol of the elemnt to pass creat Atoms object default is “H” for hydrogen

• symbol – Symbol of the elemnt to pass creat Atoms object

• hard_core (float) – Type of the dislocatino core if True then -u (sign of displacement is flipped) is applied. Default is False i.e. soft core is created.

• center (tuple of floats) – Coordinates of dislocation core (center) (x, y, z). Default is (0., 0., 0.)

Returns:

Atoms object with predicted tetrahedral positions around dislocation core.

Return type:

ase.Atoms object

class matscipy.dislocation.BodyCenteredCubicTetrahedralFactory

Bases: SimpleCubicFactory

A factory for creating tetrahedral lattices in bcc structure

xtal_name = 'bcc_tetrahedral'

bravais_basis: Sequence[Sequence[float]] | None = [[0.0, 0.5, 0.25], [0.0, 0.5, 0.75], [0.0, 0.25, 0.5], [0.0, 0.75, 0.5], [0.5, 0.0, 0.75], [0.25, 0.0, 0.5], [0.75, 0.0, 0.5], [0.5, 0.0, 0.25], [0.5, 0.25, 0.0], [0.5, 0.75, 0.0], [0.25, 0.5, 0.0], [0.75, 0.5, 0.0]]

align()

Align the first axis along x-axis and the second in the x-y plane.

atoms_in_unit_cell = 1

basis_factor = 1.0

calc_num_atoms()

check_basis_volume()

Check the volume of the unit cell.

chop_tolerance = 1e-10

convert_to_natural_basis()

Convert directions and miller indices to the natural basis.

element_basis: Sequence[int] | None = None

find_directions(directions, miller)

Find missing directions and miller indices from the specified ones.

find_ortho(idx)

Replace keyword ‘ortho’ or ‘orthogonal’ with a direction.

get_lattice_constant()

Get the lattice constant of an element with cubic crystal structure.

inside(point)

Is a point inside the unit cell?

int_basis = array([[1, 0, 0],        [0, 1, 0],        [0, 0, 1]])

inverse_basis = array([[1, 0, 0],        [0, 1, 0],        [0, 0, 1]])

inverse_basis_factor = 1.0

make_crystal_basis()

Make the basis matrix for the crystal unit cell and the system unit cell.

make_list_of_atoms()

Repeat the unit cell.

make_unit_cell()

Make the unit cell.

other = {0: (1, 2), 1: (2, 0), 2: (0, 1)}

print_directions_and_miller(txt='')

Print direction vectors and Miller indices.

process_element(element)

Extract atomic number from element

put_atom(point)

Place an atom given its integer coordinates.

class matscipy.dislocation.BodyCenteredCubicOctahedralFactory

Bases: SimpleCubicFactory

A factory for creating octahedral lattices in bcc structure

xtal_name = 'bcc_octahedral'

bravais_basis: Sequence[Sequence[float]] | None = [[0.5, 0.5, 0.0], [0.0, 0.0, 0.5], [0.5, 0.0, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.0], [0.0, 0.5, 0.5]]

align()

Align the first axis along x-axis and the second in the x-y plane.

atoms_in_unit_cell = 1

basis_factor = 1.0

calc_num_atoms()

check_basis_volume()

Check the volume of the unit cell.

chop_tolerance = 1e-10

convert_to_natural_basis()

Convert directions and miller indices to the natural basis.

element_basis: Sequence[int] | None = None

find_directions(directions, miller)

Find missing directions and miller indices from the specified ones.

find_ortho(idx)

Replace keyword ‘ortho’ or ‘orthogonal’ with a direction.

get_lattice_constant()

Get the lattice constant of an element with cubic crystal structure.

inside(point)

Is a point inside the unit cell?

int_basis = array([[1, 0, 0],        [0, 1, 0],        [0, 0, 1]])

inverse_basis = array([[1, 0, 0],        [0, 1, 0],        [0, 0, 1]])

inverse_basis_factor = 1.0

make_crystal_basis()

Make the basis matrix for the crystal unit cell and the system unit cell.

make_list_of_atoms()

Repeat the unit cell.

make_unit_cell()

Make the unit cell.

other = {0: (1, 2), 1: (2, 0), 2: (0, 1)}

print_directions_and_miller(txt='')

Print direction vectors and Miller indices.

process_element(element)

Extract atomic number from element

put_atom(point)

Place an atom given its integer coordinates.

matscipy.dislocation.dipole_displacement_angle(W_bulk, dislo_coord_left, dislo_coord_right, shift=0.0, mode=1.0)

Generates a simple displacement field for two dislocations in a dipole configuration uding simple Voltera solution as u = b/2 * angle

matscipy.dislocation.get_u_img(W_bulk, dislo_coord_left, dislo_coord_right, n_img=10, n1_shift=0, n2_shift=0)

Function for getting displacemnt filed for images of quadrupole cells used by make_screw_quadrupole

matscipy.dislocation.make_screw_quadrupole(alat, left_shift=0, right_shift=0, n1u=5, symbol='W')

Generates a screw dislocation dipole configuration

for effective quadrupole arrangement. Works for BCC systems.

Parameters:

• alat (float) – Lattice parameter of the system in Angstrom.

• left_shift (float, optional) – Shift of the left dislocation core in number of dsitances to next equivalent disocation core positions needed for creation for final configuration for NEB. Default is 0.

• right_shift (float, optional) – shift of the right dislocation core in number of dsitances to next equivalent disocation core positions needed for creation for final configuration for NEB. Default is 0.

• n1u (int, odd number) – odd number! length of the cell a doubled distance between core along x. Main parameter to calculate cell vectors

• symbol (string) – Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory default is “W” for tungsten

Returns:

• disloc_quadrupole (ase.Atoms) – Resulting quadrupole configuration.

• W_bulk (ase.Atoms) – Perfect system.

• dislo_coord_left (list of float) – Coodrinates of left dislocation core [x, y]

• dislo_coord_right (list of float) – Coodrinates of right dislocation core [x, y]

Notes

Calculation of cell vectors

From [1] we take:

• Unit vectors for the cell are:

\[u = \frac{1}{3}[1 \bar{2} 1];\]

\[v = \frac{1}{3}[2 \bar{1} \bar{1}];\]

\[z = b = \frac{1}{2}[1 1 1];\]

• Cell vectors are:

\[C_1 = n^u_1 u + n^v_1 v + C^z_1 z;\]

\[C_2 = n^u_2 u + n^v_2 v + C^z_2 z;\]

\[C_3 = z\]

• For quadrupole arrangement n1u needs to be odd number, for 135 atoms cell we take n1u=5

• To have quadrupole as as close as possible to a square one has to take:

\[2 n^u_2 + n^v_2 = n^u_1\]

\[n^v_2 \approx \frac{n^u_1}{\sqrt{3}}\]

• for n1u = 5:

\[n^v_2 \approx \frac{n^u_1}{\sqrt{3}} = 2.89 \approx 3.0\]

\[n^u_2 = \frac{1}{2} (n^u_1 - n^v_2) \approx \frac{1}{2} (5-3)=1\]

• Following [2] cell geometry is optimized by ading tilt compomemts

Cz1 and Cz2 for our case of n1u = 3n - 1:

Easy core

\[C^z_1 = + \frac{1}{3}\]

\[C^z_2 = + \frac{1}{6}\]

Hard core

\[C^z_1 = + \frac{1}{3}\]

\[C^z_2 = + \frac{1}{6}\]

may be typo in the paper check the original!

References:

[1]

Ventelon, L. & Willaime, F. J ‘Core structure and Peierls potential of screw dislocations in alpha-Fe from first principles: cluster versus dipole approaches’ Computer-Aided Mater Des (2007) 14(Suppl 1): 85. https://doi.org/10.1007/s10820-007-9064-y

[2]

Cai W. (2005) Modeling Dislocations Using a Periodic Cell. In: Yip S. (eds) Handbook of Materials Modeling. Springer, Dordrecht https://link.springer.com/chapter/10.1007/978-1-4020-3286-8_42

matscipy.dislocation.make_screw_quadrupole_kink(alat, kind='double', n1u=5, kink_length=20, symbol='W')

Generates kink configuration using make_screw_quadrupole() function

works for BCC structure. The method is based on paper https://doi.org/10.1016/j.jnucmat.2008.12.053

Parameters:

• alat (float) – Lattice parameter of the system in Angstrom.

• kind (string) – kind of the kink: right, left or double

• n1u (int) – Number of lattice vectors for the quadrupole cell (make_screw_quadrupole() function)

• kink_length (int) – Length of the cell per kink along b in unit of b, must be even.

• symbol (string) – Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory default is “W” for tungsten

Returns:

• kink (ase.atoms) – kink configuration

• reference_straight_disloc (ase.atoms) – reference straight dislocation configuration

• large_bulk (ase.atoms) – large bulk cell corresponding to the kink configuration

matscipy.dislocation.make_edge_cyl_001_100(a0, C11, C12, C44, cylinder_r, cutoff=5.5, tol=1e-06, symbol='W')

Function to produce consistent edge dislocation configuration.

Parameters:

• alat (float) – Lattice constant of the material.

• C11 (float) – C11 elastic constant of the material.

• C12 (float) – C12 elastic constant of the material.

• C44 (float) – C44 elastic constant of the material.

• cylinder_r (float) – Radius of cylinder of unconstrained atoms around the dislocation in angstrom.

• cutoff (float) – Potential cutoff for determenition of size of fixed atoms region (2*cutoff)

• tol (float) – Tolerance for generation of self consistent solution.

• symbol (string) – Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory default is “W” for tungsten

Returns:

• bulk (ase.Atoms object) – Bulk configuration.

• disloc (ase.Atoms object) – Dislocation configuration.

• disp (np.array) – Corresponding displacement.

matscipy.dislocation.read_dislo_QMMM(filename=None, image=None)

Reads extended xyz file with QMMM configuration Uses “region” for mapping of QM, MM and fixed atoms Sets ase.constraints.FixAtoms constraint on fixed atoms

Parameters:

• filename (path to xyz file) –

• image (image with "region" array to set up constraint and extract qm_mask) –

Returns:

• dislo_QMMM (Output ase.Atoms object) – Includes “region” array and FixAtoms constraint

• qm_mask (array mask for QM atoms mapping)

matscipy.dislocation.plot_bulk(atoms, n_planes=3, ax=None, ms=200)

Plots x, y coordinates of atoms colored according to non-equivalent planes in z plane

matscipy.dislocation.ovito_dxa_straight_dislo_info(disloc, structure='BCC', replicate_z=3)

A function to extract information from ovito dxa analysis. Current version works for 1b thick configurations containing straight dislocations.

Parameters:

• disloc (ase.Atoms) – Atoms object containing the atomic configuration to analyse

• replicate_z (int) – Specifies number of times to replicate the configuration along the dislocation line. Ovito dxa analysis needs at least 3b thick cell to work.

Returns:

Results

Return type:

np.array(position, b, line, angle)

matscipy.dislocation.get_centering_mask(atoms, radius, core_position=[0.0, 0.0, 0.0], extension=[0.0, 0.0, 0.0])

matscipy.dislocation.check_duplicates(atoms, distance=0.1)

Returns a mask of atoms that have at least one other atom closer than distance

class matscipy.dislocation.CubicCrystalDislocation(unit_cell, alat, C11, C12, C44, axes, burgers, unit_cell_core_position=None, parity=None, glide_distance=None, n_planes=None, self_consistent=None)

Bases: object

__init__(unit_cell, alat, C11, C12, C44, axes, burgers, unit_cell_core_position=None, parity=None, glide_distance=None, n_planes=None, self_consistent=None)

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

init_stroh()

set_burgers(burgers)

plot_unit_cell(ms=250, ax=None)

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

class matscipy.dislocation.BCCScrew111Dislocation(alat, C11, C12, C44, symbol='W')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='W')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.BCCEdge111Dislocation(alat, C11, C12, C44, symbol='W')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='W')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.BCCMixed111Dislocation(alat, C11, C12, C44, symbol='W')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='W')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.BCCEdge100Dislocation(alat, C11, C12, C44, symbol='W')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='W')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.BCCEdge100110Dislocation(alat, C11, C12, C44, symbol='W')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='W')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.DiamondGlide30degreePartial(alat, C11, C12, C44, symbol='C')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='C')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.DiamondGlide90degreePartial(alat, C11, C12, C44, symbol='C')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='C')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.CubicCrystalDissociatedDislocation(left_dislocation, right_dislocation, burgers)

Bases: CubicCrystalDislocation

__init__(left_dislocation, right_dislocation, burgers)

This class represents a dissociated dislocation in a cubic crystal with burgers vercor b = b_left + b_right.

Parameters:

• left_dislocation (CubicCrystalDislocation) – dislocation with b_left

• right_dislocation (CubicCrystalDislocation) – dislocation with b_right

• burgers (ndarray of 3 floats) – resulting burgers vector

Raises:

• ValueError – If resulting burgers vector burgers is not a sum of burgers vectors of left and right dislocations.

• ValueError – If one of the properties of left and righ dislocations are not the same.

build_cylinder(radius, partial_distance=0, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

Overloaded function to make dissociated dislocations. Partial distance is provided as an integer to define number of glide distances between two partials.

Parameters:

• radius (float) – radius of the cell

• partial_distance (int) – distance between partials (SF length) in number of glide distances. Default is 0 -> non dissociated dislocation with b = b_left + b_right is produced

displacements(bulk_positions, center, partial_distance=0, **kwargs)

Overloaded function to provide correct displacements for the dissociated dislocation. Partial distance is provided as an integer to define number of glide distances between two partials.

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.DiamondGlideScrew(alat, C11, C12, C44, symbol='C')

Bases: CubicCrystalDissociatedDislocation

__init__(alat, C11, C12, C44, symbol='C')

This class represents a dissociated dislocation in a cubic crystal with burgers vercor b = b_left + b_right.

Parameters:

• left_dislocation (CubicCrystalDislocation) – dislocation with b_left

• right_dislocation (CubicCrystalDislocation) – dislocation with b_right

• burgers (ndarray of 3 floats) – resulting burgers vector

Raises:

• ValueError – If resulting burgers vector burgers is not a sum of burgers vectors of left and right dislocations.

• ValueError – If one of the properties of left and righ dislocations are not the same.

build_cylinder(radius, partial_distance=0, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

Overloaded function to make dissociated dislocations. Partial distance is provided as an integer to define number of glide distances between two partials.

Parameters:

• radius (float) – radius of the cell

• partial_distance (int) – distance between partials (SF length) in number of glide distances. Default is 0 -> non dissociated dislocation with b = b_left + b_right is produced

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, partial_distance=0, **kwargs)

Overloaded function to provide correct displacements for the dissociated dislocation. Partial distance is provided as an integer to define number of glide distances between two partials.

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.DiamondGlide60Degree(alat, C11, C12, C44, symbol='C')

Bases: CubicCrystalDissociatedDislocation

__init__(alat, C11, C12, C44, symbol='C')

This class represents a dissociated dislocation in a cubic crystal with burgers vercor b = b_left + b_right.

Parameters:

• left_dislocation (CubicCrystalDislocation) – dislocation with b_left

• right_dislocation (CubicCrystalDislocation) – dislocation with b_right

• burgers (ndarray of 3 floats) – resulting burgers vector

Raises:

• ValueError – If resulting burgers vector burgers is not a sum of burgers vectors of left and right dislocations.

• ValueError – If one of the properties of left and righ dislocations are not the same.

build_cylinder(radius, partial_distance=0, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

Overloaded function to make dissociated dislocations. Partial distance is provided as an integer to define number of glide distances between two partials.

Parameters:

• radius (float) – radius of the cell

• partial_distance (int) – distance between partials (SF length) in number of glide distances. Default is 0 -> non dissociated dislocation with b = b_left + b_right is produced

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, partial_distance=0, **kwargs)

Overloaded function to provide correct displacements for the dissociated dislocation. Partial distance is provided as an integer to define number of glide distances between two partials.

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.FCCScrewShockleyPartial(alat, C11, C12, C44, symbol='Fe')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='Fe')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.FCCScrew110Dislocation(alat, C11, C12, C44, symbol='Fe')

Bases: CubicCrystalDissociatedDislocation

__init__(alat, C11, C12, C44, symbol='Fe')

This class represents a dissociated dislocation in a cubic crystal with burgers vercor b = b_left + b_right.

Parameters:

• left_dislocation (CubicCrystalDislocation) – dislocation with b_left

• right_dislocation (CubicCrystalDislocation) – dislocation with b_right

• burgers (ndarray of 3 floats) – resulting burgers vector

Raises:

• ValueError – If resulting burgers vector burgers is not a sum of burgers vectors of left and right dislocations.

• ValueError – If one of the properties of left and righ dislocations are not the same.

build_cylinder(radius, partial_distance=0, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

Overloaded function to make dissociated dislocations. Partial distance is provided as an integer to define number of glide distances between two partials.

Parameters:

• radius (float) – radius of the cell

• partial_distance (int) – distance between partials (SF length) in number of glide distances. Default is 0 -> non dissociated dislocation with b = b_left + b_right is produced

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, partial_distance=0, **kwargs)

Overloaded function to provide correct displacements for the dissociated dislocation. Partial distance is provided as an integer to define number of glide distances between two partials.

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.FCCEdgeShockleyPartial(alat, C11, C12, C44, symbol='Fe')

Bases: CubicCrystalDislocation

__init__(alat, C11, C12, C44, symbol='Fe')

This class represents a dislocation in a cubic crystal

The dislocation is defined by the crystal unit cell, elastic constants C11, C12 and C44, crystal axes, burgers vector and optional shift and parity vectors.

Parameters:

• unit_cell (unit cell to build the dislocation configuration) –

• alat (lattice constant) –

• C11 (elastic constants) –

• C12 –

• C44 –

• axes (cell axes (b is normally along z direction)) –

• burgers (burgers vector of the dislocation) –

• unit_cell_core_position (dislocation core position in the unit cell) – used to shift atomic positions to make the dislocation core the center of the cell

• parity –

• glide_distance (distance to the next equivalent) – core position in the glide direction

• n_planes (int) – number of non equivalent planes in z direction

• self_consistent (float) – default value for the displacement calculation

build_cylinder(radius, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, self_consistent=True, tol=1e-06, max_iter=100, verbose=True)

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.FCCEdge110Dislocation(alat, C11, C12, C44, symbol='Fe')

Bases: CubicCrystalDissociatedDislocation

__init__(alat, C11, C12, C44, symbol='Fe')

This class represents a dissociated dislocation in a cubic crystal with burgers vercor b = b_left + b_right.

Parameters:

• left_dislocation (CubicCrystalDislocation) – dislocation with b_left

• right_dislocation (CubicCrystalDislocation) – dislocation with b_right

• burgers (ndarray of 3 floats) – resulting burgers vector

Raises:

• ValueError – If resulting burgers vector burgers is not a sum of burgers vectors of left and right dislocations.

• ValueError – If one of the properties of left and righ dislocations are not the same.

build_cylinder(radius, partial_distance=0, core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), fix_width=10.0, self_consistent=None)

Overloaded function to make dissociated dislocations. Partial distance is provided as an integer to define number of glide distances between two partials.

Parameters:

• radius (float) – radius of the cell

• partial_distance (int) – distance between partials (SF length) in number of glide distances. Default is 0 -> non dissociated dislocation with b = b_left + b_right is produced

build_glide_configurations(radius, average_positions=False, **kwargs)

build_impurity_cylinder(disloc, impurity, radius, imp_symbol='H', core_position=array([0., 0., 0.]), extension=array([0., 0., 0.]), self_consistent=False, extra_bulk_at_core=False, core_radius=0.5, shift=array([0., 0., 0.]))

displacements(bulk_positions, center, partial_distance=0, **kwargs)

Overloaded function to provide correct displacements for the dissociated dislocation. Partial distance is provided as an integer to define number of glide distances between two partials.

init_stroh()

plot_unit_cell(ms=250, ax=None)

set_burgers(burgers)

class matscipy.dislocation.FixedLineAtoms(a, direction)

Bases: object

Constrain atoms to move along a given direction only.

__init__(a, direction)

adjust_positions(atoms, newpositions)

adjust_forces(atoms, forces)

matscipy.dislocation.gamma_line(unit_cell, calc=None, shift_dir=0, surface=2, size=[2, 2, 2], factor=15, n_dots=11, relax=True, fmax=0.01, return_images=False)

This function performs a calculation of a cross-sections in ‘shift_dir` of the generalized stacking fault (GSF) gamma surface with surface orientation. A gamma surface is defined as the energy variation when the crystal is cut along a particular plane and then one of the resulting parts is displaced along a particular direction. This quantity is related to the energy landscape of dislocations and provides data out of equilibrium, preserving the crystal state. For examples for the case of W and more details see section 4.2 and figure 2 in [J. Phys.: Condens. Matter 25 (2013) 395502 (15pp)] (http://iopscience.iop.org/0953-8984/25/39/395502)

Parameters:

• unit_cell (ase.Atoms) – Unit cell to construct gamma surface from. Should have a ase.calculator attached as calc in order to perform relaxation.

• calc (ase.calculator) – if unit_cell.calc is None set unit_cell.calc to calc

• shift_dir (int) – index of unit_cell axes to shift atoms

• surface (int) – index of unit_cell axes to be the surface normal direction

• size (list of ints) – start size of the cell

• factor (int) – factor to increase the size of the cell along the surface normal direction

• n_dots (int) – number of images along the gamma line

• relax (bool) – flag to perform relaxation

• fmax (float) – maximum force value for relaxation

• return_images (bool) – flag to control if the atomic configurations are returned together with the results

Returns:

• deltas (np.array) – shift distance of every image in Angstroms

• totens (np.array) – gamma surface energy in eV / Angstroms^2

• images (list of ase.Atoms) – images along the gamma surface. Returned if return_images is True