pymatgen.core.sites module¶

class
PeriodicSite
(atoms_n_occu, coords, lattice, to_unit_cell=False, coords_are_cartesian=False, properties=None)[source]¶ Bases:
pymatgen.core.sites.Site
,monty.json.MSONable
Extension of generic Site object to periodic systems. PeriodicSite includes a lattice system.
Create a periodic site.
Parameters:  atoms_n_occu –
Species on the site. Can be:
 A sequence of element / specie specified either as string symbols, e.g. [“Li”, “Fe2+”, “P”, …] or atomic numbers, e.g., (3, 56, …) or actual Element or Specie objects.
 List of dict of elements/species and occupancies, e.g., [{“Fe” : 0.5, “Mn”:0.5}, …]. This allows the setup of disordered structures.
 coords (3x1 array or sequence) – Coordinates of site as fractional or cartesian coordinates.
 lattice – Lattice associated with the site
 to_unit_cell (bool) – Translates fractional coordinate to the basic unit cell, i.e. all fractional coordinates satisfy 0 <= a < 1. Defaults to False.
 coords_are_cartesian (bool) – Set to True if you are providing cartesian coordinates. Defaults to False.
 properties (dict) – Properties associated with the PeriodicSite, e.g., {“magmom”:5}. Defaults to None.

a
¶ Fractional a coordinate

as_dict
(verbosity=0)[source]¶ Jsonserializable dict representation of PeriodicSite.
Parameters: verbosity (int) – Verbosity level. Default of 0 only includes the matrix representation. Set to 1 for more details such as cartesian coordinates, etc.

b
¶ Fractional b coordinate

c
¶ Fractional c coordinate

distance
(other, jimage=None)[source]¶ Get distance between two sites assuming periodic boundary conditions.
Parameters:  other (PeriodicSite) – Other site to get distance from.
 jimage (3x1 array) – Specific periodic image in terms of lattice translations, e.g., [1,0,0] implies to take periodic image that is one alattice vector away. If jimage is None, the image that is nearest to the site is found.
Returns: Distance between the two sites
Return type: distance (float)

distance_and_image
(other, jimage=None)[source]¶ Gets distance and instance between two sites assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and returns the distance and jimage indices in terms of lattice vector translations. If the index jimage of atom j is specified it returns the distance between the ith atom and the specified jimage atom, the given jimage is also returned.
Parameters:  other (PeriodicSite) – Other site to get distance from.
 jimage (3x1 array) – Specific periodic image in terms of lattice translations, e.g., [1,0,0] implies to take periodic image that is one alattice vector away. If jimage is None, the image that is nearest to the site is found.
Returns: distance and periodic lattice translations of the other site for which the distance applies.
Return type: (distance, jimage)

distance_and_image_from_frac_coords
(fcoords, jimage=None)[source]¶ Gets distance between site and a fractional coordinate assuming periodic boundary conditions. If the index jimage of two sites atom j is not specified it selects the j image nearest to the i atom and returns the distance and jimage indices in terms of lattice vector translations. If the index jimage of atom j is specified it returns the distance between the i atom and the specified jimage atom, the given jimage is also returned.
Parameters:  fcoords (3x1 array) – fcoords to get distance from.
 jimage (3x1 array) – Specific periodic image in terms of lattice translations, e.g., [1,0,0] implies to take periodic image that is one alattice vector away. If jimage is None, the image that is nearest to the site is found.
Returns: distance and periodic lattice translations of the other site for which the distance applies.
Return type: (distance, jimage)

frac_coords
¶ A copy of the fractional coordinates of the site.

classmethod
from_dict
(d, lattice=None)[source]¶ Create PeriodicSite from dict representation.
Parameters:  d (dict) – dict representation of PeriodicSite
 lattice – Optional lattice to override lattice specified in d. Useful for ensuring all sites in a structure share the same lattice.
Returns: PeriodicSite

is_periodic_image
(other, tolerance=1e08, check_lattice=True)[source]¶ Returns True if sites are periodic images of each other.
Parameters:  other (PeriodicSite) – Other site
 tolerance (float) – Tolerance to compare fractional coordinates
 check_lattice (bool) – Whether to check if the two sites have the same lattice.
Returns: True if sites are periodic images of each other.
Return type: bool

lattice
¶ The lattice associated with the site.

to_unit_cell
¶ Copy of PeriodicSite translated to the unit cell.
 atoms_n_occu –

class
Site
(atoms_n_occu, coords, properties=None)[source]¶ Bases:
_abcoll.Hashable
,monty.json.MSONable
A generalized nonperiodic site. This is essentially a composition at a point in space, with some optional properties associated with it. A Composition is used to represent the atoms and occupancy, which allows for disordered site representation. Coords are given in standard cartesian coordinates.
Create a nonperiodic site.
Parameters:  atoms_n_occu –
Species on the site. Can be: i. A Composition object (preferred) ii. An element / specie specified either as a string
symbols, e.g. “Li”, “Fe2+”, “P” or atomic numbers, e.g., 3, 56, or actual Element or Specie objects. iii.Dict of elements/species and occupancies, e.g.,
 {“Fe” : 0.5, “Mn”:0.5}. This allows the setup of disordered structures.
 coords – Cartesian coordinates of site.
 properties – Properties associated with the site as a dict, e.g. {“magmom”: 5}. Defaults to None.

coords
¶ A copy of the cartesian coordinates of the site as a numpy array.

distance
(other)[source]¶ Get distance between two sites.
Parameters: other – Other site. Returns: Distance (float)

distance_from_point
(pt)[source]¶ Returns distance between the site and a point in space.
Parameters: pt – Cartesian coordinates of point. Returns: Distance (float)

is_ordered
¶ True if site is an ordered site, i.e., with a single species with occupancy 1.

position_atol
= 1e05¶

properties
¶ Returns a view of properties as a dict.

specie
¶ The Specie/Element at the site. Only works for ordered sites. Otherwise an AttributeError is raised. Use this property sparingly. Robust design should make use of the property species_and_occu instead.
Raises: AttributeError if Site is not ordered.

species_and_occu
¶ The species at the site, i.e., a Composition mapping type of element/species to occupancy.

species_string
¶ String representation of species on the site.

x
¶ Cartesian x coordinate

y
¶ Cartesian y coordinate

z
¶ Cartesian z coordinate
 atoms_n_occu –