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, high_symmetry_points=None, **qwargs)[source]

Bases: object

The Atoms class represents all the information required to describe a structure at the atomic scale. This class is written in such a way that is compatible with the ASE atoms class. Some of the functions in this module is based on the corresponding implementation in the ASE package

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_tag(*args, **qwargs)[source]

Add tags to the atoms object.

Examples

For selective dynamics:

>>> self.add_tag(selective_dynamics=[False, False, False])
analyse_ovito_centro_symmetry(num_neighbors=12)[source]
analyse_ovito_cna_adaptive(mode='total')[source]

Use Ovito’s common neighbor analysis binding.

Parameters:mode ("total"/"numeric"/"str") – Controls the style and level of detail of the output. (Default is “total”, only return a summary of the values in the structure.)
Returns:(depends on mode)
analyse_ovito_voronoi_volume()[source]
analyse_phonopy_equivalent_atoms()[source]
analyse_pyscal_steinhardt_parameter(cutoff=3.5, n_clusters=2, q=[4, 6])[source]
append(atom)[source]

Append atom to end. Copied from ase

Parameters:atom

Returns:

cell

A size 3x3 array which gives the lattice vectors of the cell as [a1, a2, a3]

Type:numpy.ndarray
center(vacuum=None, axis=(0, 1, 2))[source]

Center atoms in unit cell.

Adopted from ASE code (https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.center)

Parameters:
  • vacuum (float) – If specified adjust the amount of vacuum when centering. If vacuum=10.0 there will thus be 10 Angstrom of vacuum on each side.
  • axis (tuple/list) – List or turple of integers specifying the axis along which the atoms should be centered
center_coordinates_in_unit_cell(origin=0, eps=0.0001)[source]

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()[source]
cluster_analysis(id_list, neighbors=None, radius=None, return_cluster_sizes=False)[source]
Parameters:
  • id_list
  • neighbors
  • radius
  • return_cluster_sizes

Returns:

convert_element(el, pse=None)[source]

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)[source]
Parameters:elements

Returns:

copy()[source]

Returns a copy of the instance

Returns:A copy of the instance
Return type:pyiron.atomistics.structure.atoms.Atoms
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)[source]

Extend atoms object by appending atoms from other. Copied from ase

Parameters:other

Returns:

from_hdf(hdf, group_name='structure')[source]

Retrieve the object from a HDF5 file

Parameters:
Returns:

The retrieved atoms class

Return type:

pyiron_atomistic.structure.atoms.Atoms

get_array(name, copy=True)[source]

Get an array. This function is for the purpose of compatibility with the ASE package

Parameters:
  • name (str) – Name of the required array
  • copy (bool) – True if a copy of the array is to be returned
Returns:

An array of a copy of the array

get_atomic_numbers()[source]

Returns the atomic numbers of all the atoms in the structure

Returns:A list of atomic numbers
Return type:numpy.ndarray
get_bonds(radius=None, max_shells=None, prec=0.1, num_neighbors=20)[source]
Parameters:
  • radius
  • max_shells
  • prec – minimum distance between any two clusters (if smaller considered to be single cluster)
  • num_neighbors

Returns:

get_boundary_region(dist)[source]

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

Parameters:dist

Returns:

static get_calculator()[source]
get_cell(complete=False)[source]

Get the three unit cell vectors as a 3x3 ndarray.

get_center_of_mass()[source]
Returns:center of mass in A
Return type:com (float)
get_chemical_elements()[source]

Returns the list of chemical element instances

Returns:A list of chemical element instances
Return type:numpy.ndarray
get_chemical_formula()[source]

Returns the chemical formula of structure

Returns:The chemical formula as a string
Return type:str
get_chemical_indices()[source]

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

Returns:A list of chemical indices
Return type:numpy.ndarray
get_chemical_symbols()[source]

Returns the chemical symbols for all the atoms in the structure

Returns:A list of chemical symbols
Return type:numpy.ndarray
get_constraint()[source]
get_density()[source]

Returns the density in g/cm^3

Returns:Density of the structure
Return type:float
get_distance(a0, a1, mic=True, vector=False)[source]

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 – position or atom ID
  • a1 – position or atom ID
  • mic – minimum image convention (True if periodic boundary conditions should be considered)
  • vector – True, if instead of distnce the vector connecting the two positions should be returned

Returns: distance or vectors in length unit

get_distance_matrix(mic=True, vector=False)[source]

Return distances between all atoms in a matrix. cf. get_distance

get_distances(a0=None, a1=None, mic=True, vector=False)[source]

Return distance matrix of every position in p1 with every position in p2

Parameters:
  • a0 (numpy.ndarray/list) – Nx3 array of positions
  • a1 (numpy.ndarray/list) – Nx3 array of positions
  • mic (bool) – minimum image convention
  • vector (bool) – return vectors instead of distances
Returns:

numpy.ndarray NxN if vector=False and NxNx3 if vector=True

if a1 is not set, it is assumed that distances between all positions in a0 are desired. a1 will be set to a0 in this case. if both a0 and a1 are not set, the distances between all atoms in the box are returned

Use mic to use the minimum image convention.

Learn more about get_distances from the ase website: https://wiki.fysik.dtu.dk/ase/ase/geometry.html#ase.geometry.get_distances

get_equivalent_atoms(eps=1e-05)[source]
Parameters:eps

Returns:

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

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_high_symmetry_points()[source]

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

Returns:high_symmetry_points
Return type:dict
get_initial_magnetic_moments()[source]

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)[source]
Parameters:
  • mesh
  • is_shift
  • is_time_reversal
  • symprec

Returns:

get_majority_species(return_count=False)[source]

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()[source]

Returns:

get_masses_dof()[source]

Returns:

get_neighborhood(position, num_neighbors=12, t_vec=True, include_boundary=True, tolerance=2, id_list=None, cutoff=None, cutoff_radius=None)[source]
Parameters:
  • position – position in a box whose neighborhood information is analysed
  • num_neighbors
  • t_vec (bool) – True: compute distance vectors (pbc are automatically taken into account)
  • include_boundary (bool) – True: search for neighbors assuming periodic boundary conditions False is needed e.g. in plot routines to avoid showing incorrect bonds
  • tolerance (int) – tolerance (round decimal points) used for computing neighbor shells
  • id_list
  • cutoff (float/ None) – Upper bound of the distance to which the search must be done
  • cutoff_radius (float/ None) – Upper bound of the distance to which the search must be done
Returns:

Neighbors instances with the neighbor indices, distances and vectors

Return type:

pyiron.atomistics.structure.atoms.Neighbors

get_neighbors(num_neighbors=12, t_vec=True, include_boundary=True, exclude_self=True, tolerance=2, id_list=None, cutoff_radius=None, cutoff=None)[source]
Parameters:
  • num_neighbors (int) – number of neighbors
  • t_vec (bool) – True: compute distance vectors (pbc are automatically taken into account)
  • include_boundary (bool) – True: search for neighbors assuming periodic boundary conditions False is needed e.g. in plot routines to avoid showing incorrect bonds
  • exclude_self (bool) – include central __atom (i.e. distance = 0)
  • tolerance (int) – tolerance (round decimal points) used for computing neighbor shells
  • id_list
  • cutoff (float/None) – Upper bound of the distance to which the search must be done - by default search for upto 100 neighbors unless num_neighbors is defined explicitly.
  • cutoff_radius (float/None) – Upper bound of the distance to which the search must be done - by default search for upto 100 neighbors unless num_neighbors is defined explicitly.
Returns:

Neighbors instances with the neighbor indices, distances and vectors

Return type:

pyiron.atomistics.structure.atoms.Neighbors

get_number_of_atoms()[source]

Returns:

get_number_of_degrees_of_freedom()[source]

Returns:

get_number_of_species()[source]

Returns:

get_number_species_atoms()[source]

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_parent_basis()[source]

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()[source]

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_pbc()[source]

Returns a boolean array of the periodic boundary conditions along the x, y and z axis respectively

Returns:Boolean array of length 3
Return type:numpy.ndarray
get_positions()[source]

Get positions. This function is for compatability with ASE

Returns:Positions in absolute coordinates
Return type:numpy.ndarray
get_primitive_cell(symprec=1e-05, angle_tolerance=-1.0)[source]
Parameters:
  • symprec
  • angle_tolerance

Returns:

get_scaled_positions(wrap=True)[source]

Returns the scaled/relative positions

Returns:The relative positions of the atoms in the supercell
Return type:numpy.ndarray
get_shell_matrix(shell, id_list=None, restraint_matrix=None, max_num_neighbors=100)[source]
Parameters:
  • neigh_list – user defined get_neighbors (recommended if atoms are displaced from the ideal positions)
  • id_list – cf. get_neighbors
  • radius – cf. get_neighbors
  • max_num_neighbors – cf. get_neighbors
  • restraint_matrix – NxN matrix with True or False, where False will remove the entries. If an integer is given the sum of the chemical indices corresponding to the number will be set to True and the rest to False
Returns:

NxN matrix with 1 for the pairs of atoms in the given shell

get_shell_radius(shell=1, id_list=None)[source]
Parameters:
  • shell
  • id_list

Returns:

get_shells(id_list=None, max_shell=2, max_num_neighbors=100)[source]
Parameters:
  • id_list
  • max_shell
  • max_num_neighbors

Returns:

get_spacegroup(symprec=1e-05, angle_tolerance=-1.0)[source]
Parameters:
  • symprec
  • angle_tolerance

Returns:

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

get_species_objects()[source]

Returns:

get_species_symbols()[source]

Returns the symbols of the present species

Returns:List of the symbols of the species
Return type:numpy.ndarray
get_symmetry(use_magmoms=False, use_elements=True, symprec=1e-05, angle_tolerance=-1.0)[source]
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)[source]
Parameters:
  • symprec
  • angle_tolerance

Returns:

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

get_tags()[source]

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)[source]
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()[source]

Returns:

group_points_by_symmetry(points)[source]

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.

info

This dictionary is merely used to be compatible with the ASE Atoms class.

Type:dict
new_array(name, a, dtype=None, shape=None)[source]

Adding a new array to the instance. This function is for the purpose of compatibility with the ASE package

Parameters:
  • name (str) – Name of the array
  • a (list/numpy.ndarray) – The array to be added
  • dtype (type) – Data type of the array
  • shape (list/turple) – Shape of the array
numbers_to_elements(numbers)[source]

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)[source]

Replaces specified indices with a given species

pbc

A list of boolean values which gives the periodic boundary consitions along the three axes. The default value is [True, True, True]

Type:list
plot3d(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, custom_array=None, custom_3darray=None)[source]

Plot3d relies on NGLView to visualize atomic structures. Here, we construct a string in the “protein database” (“pdb”) format, then turn it into an NGLView “structure”. PDB is a white-space sensitive format, so the string snippets are carefully formatted.

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:
  • 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.)
  • 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’.
plot3d_ase(spacefill=True, show_cell=True, camera='perspective', particle_size=0.5, background='white', color_scheme='element', show_axes=True)[source]
Possible color schemes:
” “, “picking”, “random”, “uniform”, “atomindex”, “residueindex”, “chainindex”, “modelindex”, “sstruc”, “element”, “resname”, “bfactor”, “hydrophobicity”, “value”, “volume”, “occupancy”

Returns:

pop(i=-1)[source]

Remove and return atom at index i (default last).

Parameters:i

Returns:

pos_xyz()[source]

Returns:

refine_cell(symprec=1e-05, angle_tolerance=-1.0)[source]
Parameters:
  • symprec
  • angle_tolerance

Returns:

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

repeat(rep)[source]

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).

reset_absolute(is_absolute)[source]
rotate(vector, angle=None, center=(0, 0, 0), rotate_cell=False, index_list=None)[source]

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:
  • rotate_cell
  • center
  • vector (list/numpy.ndarray/string) – Vector to rotate the atoms around. Vectors can be given as strings: ‘x’, ‘-x’, ‘y’, … .
  • angle (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’.
  • = [0, 0, 0] (center) – 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('H', [[-0.1, 1.01, -0.5]], cell=[[1, 0, 0], [0, 1, 0], [0, 0, 4]], pbc=[1, 1, 0])
>>> a = (22./ 7.) / 2. # pi/2
>>> atoms.rotate('z', a)
>>> atoms.rotate((0, 0, 1), a)
>>> atoms.rotate('-z', -a)
>>> atoms.rotate((0, 0, a))
>>> atoms.rotate('x', 'y')
rotate_euler(center=(0, 0, 0), phi=0.0, theta=0.0, psi=0.0)[source]

Rotate atoms via Euler angles.

See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.

Parameters:

center :
The point to rotate about. a sequence of length 3 with the coordinates, or ‘COM’ to select the center of mass, ‘COP’ to select center of positions or ‘COU’ to select center of cell.
phi :
The 1st rotation angle around the z axis (in radian)
theta :
Rotation around the x axis (in radian)
psi :
2nd rotation around the z axis (in radian)
scaled_pos_xyz()[source]

Returns:

scaled_positions
select_index(el)[source]

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)[source]

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()[source]
set_array(name, a, dtype=None, shape=None)[source]

Update array. This function is for the purpose of compatibility with the ASE package

Parameters:
  • name (str) – Name of the array
  • a (list/numpy.ndarray) – The array to be added
  • dtype (type) – Data type of the array
  • shape (list/turple) – Shape of the array
set_cell(cell, scale_atoms=False)[source]

Set unit cell vectors.

Parameters:

cell: 3x3 matrix or length 3 or 6 vector
Unit cell. A 3x3 matrix (the three unit cell vectors) or just three numbers for an orthorhombic cell. Another option is 6 numbers, which describes unit cell with lengths of unit cell vectors and with angles between them (in degrees), in following order: [len(a), len(b), len(c), angle(b,c), angle(a,c), angle(a,b)]. First vector will lie in x-direction, second in xy-plane, and the third one in z-positive subspace.
scale_atoms: bool
Fix atomic positions or move atoms with the unit cell? Default behavior is to not move the atoms (scale_atoms=False).

Examples:

Two equivalent ways to define an orthorhombic cell:

>>> atoms = Atoms('He')
>>> a, b, c = 7, 7.5, 8
>>> atoms.set_cell([a, b, c])
>>> atoms.set_cell([(a, 0, 0), (0, b, 0), (0, 0, c)])

FCC unit cell:

>>> atoms.set_cell([(0, b, b), (b, 0, b), (b, b, 0)])

Hexagonal unit cell:

>>> atoms.set_cell([a, a, c, 90, 90, 120])

Rhombohedral unit cell:

>>> alpha = 77
>>> atoms.set_cell([a, a, a, alpha, alpha, alpha])
set_constraint(constrain)[source]
set_high_symmetry_points(new_high_symmetry_points)[source]

Sets new high symmetry points dictionary.

Parameters:new_high_symmetry_points (dict) – new high symmetry points
set_initial_magnetic_moments(magmoms)[source]

Set array of initial magnetic moments.

Parameters:magmoms (numpy.array()) –
set_pbc(value)[source]

Sets the perioic boundary conditions on all three axis

Parameters:value (numpy.ndarray/list) – An array of bool type with length 3
set_positions(positions)[source]

Set positions. This function is for compatability with ASE

Parameters:positions (numpy.ndarray/list) – Positions in absolute coordinates
set_relative()[source]
set_repeat(vec)[source]
set_scaled_positions(scaled)[source]

Set positions relative to unit cell.

Parameters:scaled (numpy.ndarray/list) – The relative coordinates
set_species(value)[source]

Setting the species list

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

A list of atomistics.structure.periodic_table.ChemicalElement instances

Type:list
to_hdf(hdf, group_name='structure')[source]

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
translate(displacement)[source]

Translate atomic positions.

The displacement argument can be a float, an xyz vector, or an nx3 array (where n is the number of atoms).

Parameters:displacement

Returns:

wrap(center=(0.5, 0.5, 0.5), pbc=None, eps=1e-07)[source]

Wrap positions to unit cell.

Parameters:

center: three float
The positons in fractional coordinates that the new positions will be nearest possible to.
pbc: one or 3 bool
For each axis in the unit cell decides whether the positions will be moved along this axis. By default, the boundary conditions of the Atoms object will be used.
eps: float
Small number to prevent slightly negative coordinates from beeing wrapped.

See also the ase.utils.geometry.wrap_positions() function. Example:

>>> a = Atoms('H',
...           [[-0.1, 1.01, -0.5]],
...           cell=[[1, 0, 0], [0, 1, 0], [0, 0, 4]],
...           pbc=[1, 1, 0])
>>> a.wrap()
>>> a.positions
array([[ 0.9 ,  0.01, -0.5 ]])
write(filename, format=None, **kwargs)[source]

Write atoms object to a file.

see ase.io.write for formats. kwargs are passed to ase.io.write.

Parameters:
  • filename
  • format
  • **kwargs

Returns:

class pyiron.atomistics.structure.atoms.CrystalStructure[source]

Bases: object

class pyiron.atomistics.structure.atoms.Neighbors[source]

Bases: object

Class for storage of the neighbor information for a given atom based on the KDtree algorithm

distances
indices
shells
vecs
pyiron.atomistics.structure.atoms.ase_to_pyiron(ase_obj)[source]
Parameters:ase_obj

Returns:

pyiron.atomistics.structure.atoms.default(data, dflt)[source]

Helper function for setting default values.

Parameters:
  • data
  • dflt

Returns:

pyiron.atomistics.structure.atoms.ovito_to_pyiron(ovito_obj)[source]
Parameters:ovito_obj

Returns:

pyiron.atomistics.structure.atoms.pyiron_to_ase(pyiron_obj)[source]
pyiron.atomistics.structure.atoms.pyiron_to_ovito(atoms)[source]
Parameters:atoms

Returns:

pyiron.atomistics.structure.atoms.pyiron_to_pymatgen(pyiron_obj)[source]

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)[source]

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)[source]

Convert string to list of chemical symbols.

Parameters:s

Returns:

pyiron.atomistics.structure.atoms.string2vector(v)[source]
Parameters:v

Returns:

pyiron.atomistics.structure.atoms.symbols2numbers(symbols)[source]
Parameters:symbols (list, str) –

Returns: