pyiron.atomistics.structure.atoms module

class pyiron.atomistics.structure.atoms.Atoms(symbols=None, positions=None, numbers=None, tags=None, momenta=None, masses=None, magmoms=None, charges=None, scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None, calculator=None, info=None, indices=None, elements=None, dimension=None, species=None, **qwargs)

Bases: ase.atoms.Atoms

The Atoms class represents all the information required to describe a structure at the atomic scale. This class is derived from the ASE atoms class.

Parameters

• elements (list/numpy.ndarray) – List of strings containing the elements or a list of atomistics.structure.periodic_table.ChemicalElement instances

• numbers (list/numpy.ndarray) – List of atomic numbers of elements

• symbols (list/numpy.ndarray) – List of chemical symbols

• positions (list/numpy.ndarray) – List of positions

• scaled_positions (list/numpy.ndarray) – List of scaled positions (relative coordinates)

• pbc (list/numpy.ndarray/boolean) – Tells if periodic boundary conditions should be applied on the three axes

• cell (list/numpy.ndarray instance) – A 3x3 array representing the lattice vectors of the structure

Note: Only one of elements/symbols or numbers should be assigned during initialization

indices

A list of size N which gives the species index of the structure which has N atoms

Type

numpy.ndarray

add_high_symmetry_path(path)

Adds a new path to the dictionary of pathes for band structure calculations.

Parameters

path (dict) – dictionary of lists of tuples with start and end point. E.G. {“my_path”: [(‘Gamma’, ‘X’), (‘X’, ‘Y’)]}

add_high_symmetry_points(new_points)

Adds new points to the dict of existing high symmetry points.

Parameters

new_points (dict) – Points to add

add_tag(*args, **qwargs)

Add tags to the atoms object.

Examples

For selective dynamics:

>>> self.add_tag(selective_dynamics=[False, False, False])

property analyse

analyse_ovito_centro_symmetry(num_neighbors=12)

Analyse centrosymmetry parameter

Parameters

num_neighbors (int) – number of neighbors

Returns

list of centrosymmetry parameter

Return type

list

analyse_ovito_cna_adaptive(mode='total')

Use common neighbor analysis

Parameters

• mode ("total"/"numeric"/"str") –

  Controls the style and level of detail of the output. - total : return number of atoms belonging to each structure - numeric : return a per atom list of numbers- 0 for unknown,

  1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• ovito_compatibility (bool) – use ovito compatiblity mode

Returns

(depends on mode)

analyse_ovito_voronoi_volume()

Calculate the Voronoi volume of atoms

analyse_phonopy_equivalent_atoms()

analyse_pyscal_centro_symmetry(num_neighbors=12)

Analyse centrosymmetry parameter

Parameters

num_neighbors (int) – number of neighbors

Returns

list of centrosymmetry parameter

Return type

list

analyse_pyscal_cna_adaptive(mode='total', ovito_compatibility=False)

Use common neighbor analysis

Parameters

• mode ("total"/"numeric"/"str") –

  Controls the style and level of detail of the output. - total : return number of atoms belonging to each structure - numeric : return a per atom list of numbers- 0 for unknown,

  1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• ovito_compatibility (bool) – use ovito compatiblity mode

Returns

(depends on mode)

analyse_pyscal_diamond_structure(mode='total', ovito_compatibility=False)

Analyse diamond structure

Parameters

• mode ("total"/"numeric"/"str") – Controls the style and level

• detail of the output. (of) –

  • total : return number of atoms belonging to each structure

  • numericreturn a per atom list of numbers- 0 for unknown,

    1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• ovito_compatibility (bool) – use ovito compatiblity mode

Returns

(depends on mode)

analyse_pyscal_steinhardt_parameter(neighbor_method='cutoff', cutoff=0, n_clusters=2, q=(4, 6), averaged=False, clustering=True)

Calculate Steinhardts parameters

Parameters

• neighbor_method (str) – can be [‘cutoff’, ‘voronoi’]

• cutoff (float) – can be 0 for adaptive cutoff or any other value

• n_clusters (int) – number of clusters for K means clustering

• q (list) – can be from 2-12, the required q values to be calculated

• averaged (bool) – If True, calculates the averaged versions of the parameter

• clustering (bool) – If True, cluster based on the q values

Returns

calculated q parameters

Return type

list

analyse_pyscal_voronoi_volume()

Calculate the Voronoi volume of atoms

append(atom)

Append atom to end.

apply_strain(epsilon, return_box=False)

Apply a given strain on the structure

Parameters

• epsilon (float/list/ndarray) – epsilon matrix. If a single number is set, the same strain is applied in each direction. If a 3-dim vector is set, it will be multiplied by a unit matrix.

• return_box (bool) – whether to return a box. If set to True, only the returned box will have the desired strain and the original box will stay unchanged.

center_coordinates_in_unit_cell(origin=0, eps=0.0001)

Wrap atomic coordinates within the supercell as given by a1, a2., a3

Parameters

• origin (float) – 0 to confine between 0 and 1, -0.5 to confine between -0.5 and 0.5

• eps (float) – Tolerance to detect atoms at cell edges

Returns

Wrapped structure

Return type

pyiron.atomistics.structure.atoms.Atoms

close()

cluster_analysis(id_list, neighbors=None, radius=None, return_cluster_sizes=False)

Parameters

• id_list –

• neighbors –

• radius –

• return_cluster_sizes –

Returns:

convert_element(el, pse=None)

Convert a string or an atom instance into a ChemicalElement instance

Parameters

• el (str/atomistics.structure.atom.Atom) – String or atom instance from which the element should be generated

• pse (atomistics.structure.periodictable.PeriodicTable) – PeriodicTable instance from which the element is generated (optional)

Returns

The required chemical element

Return type

atomistics.structure.periodictable.ChemicalElement

static convert_formula(elements)

Convert a given chemical formula into a list of elements

Parameters

elements (str) – A string of the required chamical formula (eg. H2O)

Returns

A list of elements corresponding to the formula

Return type

list

copy()

Returns a copy of the instance

Returns

A copy of the instance

Return type

pyiron.atomistics.structure.atoms.Atoms

create_line_mode_structure(with_time_reversal=True, recipe='hpkot', threshold=1e-07, symprec=1e-05, angle_tolerance=- 1.0)

Uses ‘seekpath’ to create a new structure with high symmetry points and path for band structure calculations.

Parameters

• with_time_reversal (bool) – if False, and the group has no inversion symmetry, additional lines are returned as described in the HPKOT paper.

• recipe (str) – choose the reference publication that defines the special points and paths. Currently, only ‘hpkot’ is implemented.

• threshold (float) – the threshold to use to verify if we are in and edge case (e.g., a tetragonal cell, but a==c). For instance, in the tI lattice, if abs(a-c) < threshold, a EdgeCaseWarning is issued. Note that depending on the bravais lattice, the meaning of the threshold is different (angle, length, …)

• symprec (float) – the symmetry precision used internally by SPGLIB

• angle_tolerance (float) – the angle_tolerance used internally by SPGLIB

Returns

new structure

Return type

pyiron.atomistics.structure.atoms.Atoms

property elements

A size N list of atomistics.structure.periodic_table.ChemicalElement instances according to the ordering of the atoms in the instance

Type

numpy.ndarray

extend(other)

Extend atoms object by appending atoms from other. (Extending the ASE function)

Parameters

other (pyiron.atomistics.structure.atoms.Atoms/ase.atoms.Atoms) – Structure to append

Returns

The extended structure

Return type

pyiron.atomistics.structure.atoms.Atoms

find_mic(v, vectors=True)

Find vectors following minimum image convention (mic). In principle this function does the same as ase.geometry.find_mic

Parameters

• v (list/numpy.ndarray) – 3d vector or a list/array of 3d vectors

• vectors (bool) – Whether to return vectors (distances are returned if False)

Returns: numpy.ndarray of the same shape as input with mic

find_neighbors_by_vector(vector, return_deviation=False, num_neighbors=96)

Parameters

• vector (list/np.ndarray) – vector by which positions are translated (and neighbors are searched)

• return_deviation (bool) – whether to return distance between the expect positions and real positions

Returns

list of id’s for the specified translation

Return type

np.ndarray

Example

a_0 = 2.832 structure = pr.create_structure(‘Fe’, ‘bcc’, a_0) id_list = structure.find_neighbors_by_vector([0, 0, a_0]) # In this example, you get a list of neighbor atom id’s at z+=a_0 for each atom. # This is particularly powerful for SSA when the magnetic structure has to be translated # in each direction.

from_hdf(hdf, group_name='structure')

Retrieve the object from a HDF5 file

Parameters

• hdf (pyiron_base.generic.hdfio.FileHDFio) – HDF path to which the object is to be saved

• group_name (str) – Group name from which the Atoms object is retreived.

Returns

The retrieved atoms class

Return type

pyiron_atomistic.structure.atoms.Atoms

get_atomic_numbers()

Returns the atomic numbers of all the atoms in the structure

Returns

A list of atomic numbers

Return type

numpy.ndarray

get_bonds(radius=inf, max_shells=None, prec=0.1, num_neighbors=20)

Parameters

• radius –

• max_shells –

• prec – minimum distance between any two clusters (if smaller considered to be single cluster)

• num_neighbors –

Returns:

get_center_of_mass()

Returns

center of mass in A

Return type

com (float)

get_chemical_elements()

Returns the list of chemical element instances

Returns

A list of chemical element instances

Return type

numpy.ndarray

get_chemical_formula()

Returns the chemical formula of structure

Returns

The chemical formula as a string

Return type

str

get_chemical_indices()

Returns the list of chemical indices as ordered in self.species

Returns

A list of chemical indices

Return type

numpy.ndarray

get_chemical_symbols()

Returns the chemical symbols for all the atoms in the structure

Returns

A list of chemical symbols

Return type

numpy.ndarray

get_constraint()

get_density()

Returns the density in g/cm^3

Returns

Density of the structure

Return type

float

get_distance(a0, a1, mic=True, vector=False)

Return distance between two atoms. Use mic=True to use the Minimum Image Convention. vector=True gives the distance vector (from a0 to a1).

Parameters

• a0 (int/numpy.ndarray/list) – position or atom ID

• a1 (int/numpy.ndarray/list) – position or atom ID

• mic (bool) – minimum image convention (True if periodic boundary conditions should be considered)

• vector (bool) – True, if instead of distnce the vector connecting the two positions should be returned

Returns

distance or vectors in length unit

Return type

float

get_distances_array(p1=None, p2=None, mic=True, vectors=False)

Return distance matrix of every position in p1 with every position in p2. If p2 is not set, it is assumed that distances between all positions in p1 are desired. p2 will be set to p1 in this case. If both p1 and p2 are not set, the distances between all atoms in the box are returned.

Parameters

• p1 (numpy.ndarray/list) – Nx3 array of positions

• p2 (numpy.ndarray/list) – Nx3 array of positions

• mic (bool) – minimum image convention

• vectors (bool) – return vectors instead of distances

Returns

NxN if vector=False and NxNx3 if vector=True

Return type

numpy.ndarray

get_equivalent_points(points, use_magmoms=False, use_elements=True, symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• points (list/ndarray) – 3d vector

• use_magmoms (bool) – cf. get_symmetry()

• use_elements (bool) – cf. get_symmetry()

• symprec (float) – cf. get_symmetry()

• angle_tolerance (float) – cf. get_symmetry()

Returns

array of equivalent points with respect to box symmetries

Return type

(ndarray)

get_equivalent_voronoi_vertices(return_box=False, minimum_dist=0.1, symprec=1e-05, angle_tolerance=- 1.0)

This function gives the positions of spatially equivalent Voronoi vertices in lists, which most likely represent interstitial points or vacancies (along with other high symmetry points) Each list item contains an array of positions which are spacially equivalent. This function does not work if there are Hs atoms in the box

Parameters

• return_box – True, if the box containing atoms on the positions of Voronoi vertices should be returned (which are represented by Hs atoms)

• minimum_dist – Minimum distance between two Voronoi vertices to be considered as one

Returns: List of numpy array positions of spacially equivalent Voronoi vertices

get_extended_positions(width, return_indices=False, norm_order=2)

Get all atoms in the boundary around the supercell which have a distance to the supercell boundary of less than dist

Parameters

• width (float) – width of the buffer layer on every periodic box side within which all atoms across periodic boundaries are chosen.

• return_indices (bool) – Whether or not return the original indices of the appended atoms.

• norm_order (float) – Order of Lp-norm.

Returns

Positions of all atoms in the extended box, indices of atoms in

their original option (if return_indices=True)

Return type

numpy.ndarray

get_high_symmetry_path()

Path used for band structure calculations

Returns

dict of pathes with start and end points.

Return type

dict

get_high_symmetry_points()

dictionary of high-symmetry points defined for this specific structure.

Returns

high_symmetry_points

Return type

dict

get_initial_magnetic_moments()

Get array of initial magnetic moments.

Returns

numpy.array()

get_ir_reciprocal_mesh(mesh, is_shift=array([0, 0, 0], dtype=int32), is_time_reversal=True, symprec=1e-05)

Parameters

• mesh –

• is_shift –

• is_time_reversal –

• symprec –

Returns:

get_majority_species(return_count=False)

This function returns the majority species and their number in the box

Returns

number of atoms of the majority species, chemical symbol and chemical index

get_masses()

Gets the atomic masses of all atoms in the structure

Returns

Array of masses

Return type

numpy.ndarray

get_masses_dof()

Returns:

get_neighborhood(positions, num_neighbors=12, t_vec=True, cutoff_radius=inf, width_buffer=1.2, norm_order=2)

Parameters

• position – Position in a box whose neighborhood information is analysed

• num_neighbors (int) – Number of nearest neighbors

• t_vec (bool) – True: compute distance vectors (pbc are taken into account)

• cutoff_radius (float) – Upper bound of the distance to which the search is to be done

• width_buffer (float) – Width of the layer to be added to account for pbc.

• norm_order (int) – Norm to use for the neighborhood search and shell recognition. The definition follows the conventional Lp norm (cf. https://en.wikipedia.org/wiki/Lp_space). This is an feature and for anything other than norm_order=2, there is no guarantee that this works flawlessly.

Returns

Neighbors instances with the neighbor

indices, distances and vectors

Return type

pyiron.atomistics.structure.atoms.Tree

get_neighbors(num_neighbors=12, t_vec=True, tolerance=2, id_list=None, cutoff_radius=inf, width_buffer=1.2, allow_ragged=False, norm_order=2)

Parameters

• num_neighbors (int) – number of neighbors

• t_vec (bool) – True: compute distance vectors (pbc are automatically taken into account)

• tolerance (int) – tolerance (round decimal points) used for computing neighbor shells

• id_list (list) – list of atoms the neighbors are to be looked for

• cutoff_radius (float) – Upper bound of the distance to which the search must be done

• width_buffer (float) – width of the layer to be added to account for pbc.

• allow_ragged (bool) – Whether to allow ragged list of arrays or rectangular numpy.ndarray filled with np.inf for values outside cutoff_radius

• norm_order (int) – Norm to use for the neighborhood search and shell recognition. The definition follows the conventional Lp norm (cf. https://en.wikipedia.org/wiki/Lp_space). This is an feature and for anything other than norm_order=2, there is no guarantee that this works flawlessly.

Returns

Neighbors instances with the neighbor

indices, distances and vectors

Return type

pyiron.atomistics.structure.atoms.Neighbors

get_neighbors_by_distance(cutoff_radius=5, num_neighbors=None, t_vec=True, tolerance=2, id_list=None, width_buffer=1.2, allow_ragged=True, norm_order=2)

Parameters

• cutoff_radius (float) – Upper bound of the distance to which the search must be done

• num_neighbors (int/None) – maximum number of neighbors found; if None this is estimated based on the density.

• t_vec (bool) – True: compute distance vectors (pbc are automatically taken into account)

• tolerance (int) – tolerance (round decimal points) used for computing neighbor shells

• id_list (list) – list of atoms the neighbors are to be looked for

• width_buffer (float) – width of the layer to be added to account for pbc.

• allow_ragged (bool) – Whether to allow ragged list of arrays or rectangular numpy.ndarray filled with np.inf for values outside cutoff_radius

• norm_order (int) – Norm to use for the neighborhood search and shell recognition. The definition follows the conventional Lp norm (cf. https://en.wikipedia.org/wiki/Lp_space). This is an feature and for anything other than norm_order=2, there is no guarantee that this works flawlessly.

Returns

Neighbors instances with the neighbor

indices, distances and vectors

Return type

pyiron.atomistics.structure.atoms.Neighbors

get_number_of_atoms()

Returns:

get_number_of_degrees_of_freedom()

Returns:

get_number_of_species()

Returns:

get_number_species_atoms()

Returns a dictionary with the species in the structure and the corresponding count in the structure

Returns

An ordered dictionary with the species and the corresponding count

Return type

collections.OrderedDict

get_numbers_of_neighbors_in_sphere(cutoff_radius=10, num_neighbors=None, id_list=None, width_buffer=1.2)

Function to compute the maximum number of neighbors in a sphere around each atom. :param cutoff_radius: Upper bound of the distance to which the search must be done :type cutoff_radius: float :param num_neighbors: maximum number of neighbors found :type num_neighbors: int/None :param id_list: list of atoms the neighbors are to be looked for :type id_list: list :param width_buffer: width of the layer to be added to account for pbc. :type width_buffer: float

Returns

for each atom the number of neighbors found in the sphere of radius

cutoff_radius (<= num_neighbors if specified)

Return type

(np.ndarray)

get_parent_basis()

Returns the basis with all user defined/special elements as the it’s parent

Returns

Structure without any user defined elements

Return type

pyiron.atomistics.structure.atoms.Atoms

get_parent_symbols()

Returns the chemical symbols for all the atoms in the structure even for user defined elements

Returns

A list of chemical symbols

Return type

numpy.ndarray

get_primitive_cell(symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• symprec –

• angle_tolerance –

Returns:

get_shell_matrix(id_list=None, chemical_pair=None, num_neighbors=100, tolerance=2, cluster_by_distances=False, cluster_by_vecs=False)

Shell matrices for pairwise interaction. Note: The matrices are always symmetric, meaning if you use them as bilinear operators, you have to divide the results by 2.

Parameters

chemical_pair (list) – pair of chemical symbols (e.g. [‘Fe’, ‘Ni’])

Returns

list of sparse matrices for different shells

Example

from pyiron import Project structure = Project(‘.’).create_structure(‘Fe’, ‘bcc’, 2.83).repeat(2) J = -0.1 # Ising parameter magmoms = 2*np.random.random((len(structure)), 3)-1 # Random magnetic moments between -1 and 1 neigh = structure.get_neighbors(num_neighbors=8) # Iron first shell shell_matrices = neigh.get_shell_matrix() print(‘Energy =’, 0.5*J*magmoms.dot(shell_matrices[0].dot(matmoms)))

get_spacegroup(symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• symprec –

• angle_tolerance –

Returns:

https://atztogo.github.io/spglib/python-spglib.html

get_species_objects()

Returns:

get_species_symbols()

Returns the symbols of the present species

Returns

List of the symbols of the species

Return type

numpy.ndarray

get_spherical_coordinates(x=None)

Parameters

x (list/ndarray) – coordinates to transform. If not set, the positions in structure will be returned.

Returns

array in spherical coordinates

get_symmetry(use_magmoms=False, use_elements=True, symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• use_magmoms –

• use_elements – True or False. If False, chemical elements will be ignored

• symprec –

• angle_tolerance –

Returns:

get_symmetry_dataset(symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• symprec –

• angle_tolerance –

Returns:

https://atztogo.github.io/spglib/python-spglib.html

get_tags()

Returns the keys of the stored tags of the structure

Returns

Keys of the stored tags

Return type

dict_keys

get_volume(per_atom=False)

Parameters

per_atom (bool) – True if volume per atom is to be returned

Returns

Volume in A**3

Return type

volume (float)

get_voronoi_volume()

Calculate the Voronoi volume of atoms

get_wrapped_coordinates(positions, epsilon=1e-08)

Return coordinates in wrapped in the periodic cell

Parameters

• positions (list/numpy.ndarray) – Positions

• epsilon (float) – displacement to add to avoid wrapping of atoms at borders

Returns

Wrapped positions

Return type

numpy.ndarray

group_points_by_symmetry(points)

This function classifies the points into groups according to the box symmetry given by spglib.

Parameters

points – (np.array/list) nx3 array which contains positions

Returns: list of arrays containing geometrically equivalent positions

It is possible that the original points are not found in the returned list, as the positions outsie the box will be projected back to the box.

numbers_to_elements(numbers)

Convert atomic numbers in element objects (needed for compatibility with ASE)

Parameters

numbers (list) – List of Element Numbers (as Integers; default in ASE)

Returns

A list of elements as needed for pyiron

Return type

list

occupy_lattice(**qwargs)

Replaces specified indices with a given species

plot3d(mode='NGLview', show_cell=True, show_axes=True, camera='orthographic', spacefill=True, particle_size=1.0, select_atoms=None, background='white', color_scheme=None, colors=None, scalar_field=None, scalar_start=None, scalar_end=None, scalar_cmap=None, vector_field=None, vector_color=None, magnetic_moments=False, view_plane=array([0, 0, 1]), distance_from_camera=1.0, opacity=1.0)

Plot3d relies on NGLView or plotly to visualize atomic structures. Here, we construct a string in the “protein database”

The final widget is returned. If it is assigned to a variable, the visualization is suppressed until that variable is evaluated, and in the meantime more NGL operations can be applied to it to modify the visualization.

Parameters

• mode (str) – NGLView, plotly or ase

• show_cell (bool) – Whether or not to show the frame. (Default is True.)

• show_axes (bool) – Whether or not to show xyz axes. (Default is True.)

• camera (str) – ‘perspective’ or ‘orthographic’. (Default is ‘perspective’.)

• spacefill (bool) – Whether to use a space-filling or ball-and-stick representation. (Default is True, use space-filling atoms.)

• particle_size (float) – Size of the particles. (Default is 1.)

• select_atoms (numpy.ndarray) – Indices of atoms to show, either as integers or a boolean array mask. (Default is None, show all atoms.)

• background (str) – Background color. (Default is ‘white’.)

• color_scheme (str) – NGLView color scheme to use. (Default is None, color by element.)

• colors (numpy.ndarray) – A per-atom array of HTML color names or hex color codes to use for atomic colors. (Default is None, use coloring scheme.)

• scalar_field (numpy.ndarray) – Color each atom according to the array value (Default is None, use coloring scheme.)

• scalar_start (float) – The scalar value to be mapped onto the low end of the color map (lower values are clipped). (Default is None, use the minimum value in scalar_field.)

• scalar_end (float) – The scalar value to be mapped onto the high end of the color map (higher values are clipped). (Default is None, use the maximum value in scalar_field.)

• scalar_cmap (matplotlib.cm) – The colormap to use. (Default is None, giving a blue-red divergent map.)

• vector_field (numpy.ndarray) – Add vectors (3 values) originating at each atom. (Default is None, no vectors.)

• vector_color (numpy.ndarray) – Colors for the vectors (only available with vector_field). (Default is None, vectors are colored by their direction.)

• magnetic_moments (bool) – Plot magnetic moments as ‘scalar_field’ or ‘vector_field’.

• view_plane (numpy.ndarray) – A Nx3-array (N = 1,2,3); the first 3d-component of the array specifies which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes), the second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the third component (if specified) is the vertical component, which is ignored and calculated internally. The orthonormality of the orientation is internally ensured, and therefore is not required in the function call. (Default is np.array([0, 0, 1]), which is view normal to the x-y plane.)

• distance_from_camera (float) – Distance of the camera from the structure. Higher = farther away. (Default is 14, which also seems to be the NGLView default value.)

• NGLView color schemes (Possible) – ” “, “picking”, “random”, “uniform”, “atomindex”, “residueindex”, “chainindex”, “modelindex”, “sstruc”, “element”, “resname”, “bfactor”, “hydrophobicity”, “value”, “volume”, “occupancy”

Returns

The NGLView widget itself, which can be operated on further or viewed as-is.

Return type

(nglview.NGLWidget)

Warning

• Many features only work with space-filling atoms (e.g. coloring by a scalar field).

• The colour interpretation of some hex codes is weird, e.g. ‘green’.

pos_xyz()

Returns:

refine_cell(symprec=1e-05, angle_tolerance=- 1.0)

Parameters

• symprec –

• angle_tolerance –

Returns:

https://atztogo.github.io/spglib/python-spglib.html

repeat(rep)

Create new repeated atoms object.

The rep argument should be a sequence of three positive integers like (2,3,1) or a single integer (r) equivalent to (r,r,r).

repeat_points(points, rep, centered=False)

Return points with repetition given according to periodic boundary conditions

Parameters

• points (np.ndarray/list) – xyz vector or list/array of xyz vectors

• rep (int/list/np.ndarray) – Repetition in each direction. If int is given, the same value is used for every direction

• centered (bool) – Whether the original points should be in the center of repeated points.

Returns

(np.ndarray) repeated points

reset_absolute(is_absolute)

rotate(a=0.0, v=None, center=(0, 0, 0), rotate_cell=False, index_list=None)

Rotate atoms based on a vector and an angle, or two vectors. This function is completely adopted from ASE code (https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate)

Parameters

• a (float/list) – Angle that the atoms is rotated around the vecor ‘v’. If an angle is not specified, the length of ‘v’ is used as the angle (default). The angle can also be a vector and then ‘v’ is rotated into ‘a’.

• v (list/numpy.ndarray/string) – Vector to rotate the atoms around. Vectors can be given as strings: ‘x’, ‘-x’, ‘y’, … .

• center (tuple/list/numpy.ndarray/str) – The center is kept fixed under the rotation. Use ‘COM’ to fix the center of mass, ‘COP’ to fix the center of positions or ‘COU’ to fix the center of cell.

• = False (rotate_cell) – If true the cell is also rotated.

• index_list (list/numpy.ndarray) – Indices of atoms to be rotated

Examples:

Rotate 90 degrees around the z-axis, so that the x-axis is rotated into the y-axis:

>>> atoms = Atoms()
>>> atoms.rotate(90, 'z')
>>> atoms.rotate(90, (0, 0, 1))
>>> atoms.rotate(-90, '-z')
>>> atoms.rotate('x', 'y')
>>> atoms.rotate((1, 0, 0), (0, 1, 0))

scaled_pos_xyz()

Returns:

select_index(el)

Returns the indices of a given element in the structure

Parameters

el (str/atomistics.structures.periodic_table.ChemicalElement/list) – Element for which the indices should be returned

Returns

An array of indices of the atoms of the given element

Return type

numpy.ndarray

select_parent_index(el)

Returns the indices of a given element in the structure ignoring user defined elements

Parameters

el (str/atomistics.structures.periodic_table.ChemicalElement) – Element for which the indices should be returned

Returns

An array of indices of the atoms of the given element

Return type

numpy.ndarray

set_absolute()

set_constraint(constraint=None)

Apply one or more constrains.

The constraint argument must be one constraint object or a list of constraint objects.

set_initial_magnetic_moments(magmoms=None)

Set array of initial magnetic moments.

Parameters

magmoms (numpy.ndarray/list) – List of magneric moments

set_relative()

set_repeat(vec)

set_species(value)

Setting the species list

Parameters

value (list) – A list atomistics.structure.periodic_table.ChemicalElement instances

property species

A list of atomistics.structure.periodic_table.ChemicalElement instances

Type

list

symmetrize_vectors(vectors, force_update=False, use_magmoms=False, use_elements=True, symprec=1e-05, angle_tolerance=- 1.0)

Symmetrization of natom x 3 vectors according to box symmetries

Parameters

• vectors (ndarray/list) – natom x 3 array to symmetrize

• force_update (bool) – whether to update the symmetry info

• use_magmoms (bool) – cf. get_symmetry

• use_elements (bool) – cf. get_symmetry

• symprec (float) – cf. get_symmetry

• angle_tolerance (float) – cf. get_symmetry

Returns

(np.ndarray) symmetrized vectors

to_hdf(hdf, group_name='structure')

Save the object in a HDF5 file

Parameters

• hdf (pyiron_base.generic.hdfio.FileHDFio) – HDF path to which the object is to be saved

• group_name (str) – Group name with which the object should be stored. This same name should be used to retrieve the object

property visualize

class pyiron.atomistics.structure.atoms.CrystalStructure(*args, **kwargs)

Bases: object

pyiron.atomistics.structure.atoms.ase_to_pyiron(ase_obj)

Convert an ase.atoms.Atoms structure object to its equivalent pyiron structure

Parameters

ase_obj (ase.atoms.Atoms) – The ase atoms instance to convert

Returns

The equivalent pyiron structure

Return type

pyiron.atomistics.structure.atoms.Atoms

pyiron.atomistics.structure.atoms.default(data, dflt)

Helper function for setting default values.

Parameters

• data –

• dflt –

Returns:

pyiron.atomistics.structure.atoms.ovito_to_pyiron(ovito_obj)

Parameters

ovito_obj –

Returns:

pyiron.atomistics.structure.atoms.pyiron_to_ase(pyiron_obj)

pyiron.atomistics.structure.atoms.pyiron_to_ovito(atoms)

Parameters

atoms –

Returns:

pyiron.atomistics.structure.atoms.pyiron_to_pymatgen(pyiron_obj)

Convert pyiron atoms object to pymatgen atoms object

Parameters

pyiron_obj – pyiron atoms object

Returns

pymatgen atoms object

pyiron.atomistics.structure.atoms.pymatgen_to_pyiron(pymatgen_obj)

Convert pymatgen atoms object to pyiron atoms object (pymatgen->ASE->pyiron)

Parameters

pymatgen_obj – pymatgen atoms object

Returns

pyiron atoms object

pyiron.atomistics.structure.atoms.string2symbols(s)

Convert string to list of chemical symbols.

Parameters

s –

Returns:

pyiron.atomistics.structure.atoms.string2vector(v)

Parameters

v –

Returns:

pyiron.atomistics.structure.atoms.symbols2numbers(symbols)

Parameters

symbols (list, str) –

Returns: