""" The site class define the properties of an atom. """
from .radial_meshes import Mesh
from .reference_systems import ReferenceSystem
import numpy as np
from ..common.decorators import cached_property
import copy
from typing import Optional, Union
[docs]
class SiteType:
"""
Definition of an atomic site.
(By symmetry) equivalent sites should share the same definition.
However, two same (by their atomic number) atoms in a spatially
different positions (i.e. not by symmetry equal) should not share
the same property.
"""
[docs]
@staticmethod
def creator(atoms):
symbols = atoms.symbols
if 'spacegroup_kinds' in atoms.arrays and 'occupancy' in atoms.info:
kinds = atoms.arrays['spacegroup_kinds']
occ = atoms.info['occupancy']
def create(index):
symbol = symbols[index]
symbol = occ.get(kinds[index], symbol)
symbol = occ.get(str(kinds[index]), symbol)
return SiteType(atoms, symbol)
else:
def create(index):
return SiteType(atoms, symbols[index])
return create
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def __init__(self, atoms, occupation, reference_system=None, mesh=None):
"""
Parameters
----------
occupation: dict
{ AtomicType: fraction }
The type of the atom
Occupation of the site. If None is given, the default occupation
of { T : 1.0 } is used, where T is determined by ASE atomic number
corresponding to the site.
atoms: SPRKKRAtoms
The atoms, into which the Site belongs
reference_system: ReferenceSystem
Default reference system is used if None is given
mesh: Mesh
Default ExponentialMesh is used if None is given
"""
self.atoms = atoms
self.reference_system = reference_system or ReferenceSystem.default()
self._mesh = mesh or Mesh.default()
self._occupation = Occupation.to_occupation(occupation, self)
self.sites = set()
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def register(self, site):
self.sites.add(site)
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def unregister(self, site):
self.sites.remove(site)
@property
def has_symmetry(self):
return len(self.sites) > 1
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def break_symmetry(self):
if not self.sites:
return
itr = iter(self.sites)
for i in itr:
i.break_symmetry()
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def _clear_data(self):
self.occupation._clear_data()
@property
def mesh(self):
return self._mesh
@mesh.setter
def mesh(self, mesh):
self.remesh(mesh)
[docs]
def remesh(self, mesh, map=None):
if map is None:
map = {}
self._mesh = mesh
self.occupation.remesh(mesh, map)
return map
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def _just_one_type(self):
if len(self.occupation) != 1:
raise ValueError("The site has multiple occupation, please use 'site_type.atomic_type(symbol/nb).desired_property'")
return self.atomic_type(0)
@property
def potential(self):
""" The radial potential data of the site, if it has one atomic type """
return self._just_one_type().potential
@potential.setter
def potential(self, value):
self._just_one_type().potential = value
@property
def charge(self):
""" The radial charge data of the site, if it has one atomic type """
return self._just_one_type().charge
@charge.setter
def charge(self, value):
self._just_one_type().charge = value
@property
def moments(self):
""" The moments data of the site, if it has one atomic type """
return self._just_one_type().moments
@moments.setter
def moments(self, value):
self._just_one_type().moments = value
[docs]
def copy(self, atoms=False, copy_mesh=True):
""" Create a copy of the site. """
mesh = self.mesh.copy() if copy_mesh else self.mesh
site_type = SiteType(self.atoms, self.occupation, # occupation will be copied
self.reference_system.copy(), mesh)
site_type._occupation._site_type = site_type
if atoms is not False:
site_type.atoms = atoms
return site_type
@property
def occupation(self):
"""
The method returns the `:class:Occupation<ase2sprkkr.sprkkr.occupations.Occupation>` - that represent
the occupation of the site by atoms. The occupation captures the probability of occurence of the
given atoms on the site. There can be only partial occupancy (the probability, that there is
an atom on the site is not 100%).
The method creates the occupation, if it not exists, according to the ASE atoms object (using occpancy and symbols)
"""
if self._occupation is None:
ids = self.index()
if not len(ids):
raise ValueError('This atomic site is not from the provided Atoms object')
atoms = self.atoms
an = atoms.get_atomic_numbers()
oc = atoms.info.get('occupancy', {})
for i in ids:
if i in oc and oc[i]:
self._occupation = Occupation(oc[i], self)
return self._occupation
for i in ids:
if an[i]:
self._occupation = Occupation(an[i], self)
return self._occupation
for i in ids:
if atoms.symbols[i]:
self._occupation = Occupation(atoms.symbols[i], self)
return self._occupation
raise ValueError('Unkwnown atom')
return self._occupation
@occupation.setter
def occupation(self, x):
self._occupation = Occupation.to_occupation(x, self)
self.update_atoms()
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def reset(self):
"""
Set the properties of the site to the default.
Currently, it resets the mesh.
"""
self.mesh = Mesh.default()
self.occupation._clear_data()
@property
def primary_symbol(self):
""" Symbol of the most important (most probable) chemical element present on the site. """
return self.occupation.primary_symbol
@property
def primary_atomic_number(self):
""" Atomic symbol of the most important (most probable) chemical element present on the site. """
return self.occupation.primary_atomic_number
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def index(self):
""" Return the the sites-array (of the owning atoms object) index for this site. """
enum = enumerate(i.site_type for i in self.atoms.sites)
return [i[0] for i in enum if i[1] is self]
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def update_atoms(self):
""" Update atomic numbers and occupation according to the sites data. """
index = self.index()
if not len(index):
return
an = self.atoms.get_atomic_numbers()
pan = self.occupation.primary_atomic_number
an[ index ] = pan
self.atoms.set_atomic_numbers(an)
occ = self.atoms.info.get('occupancy', {})
for i in index:
occ[i] = self._occupation.as_dict
self.atoms.info['occupancy'] = occ
def __str__(self):
return f"SiteType:{self.occupation}"
def __repr__(self):
return f"SiteType:{self.occupation}"
[docs]
def is_vacuum(self) -> bool:
""" Is the site vacuum pseudoatom? """
return len(self._occupation) == 1 and next(iter(self.occupation)).is_vacuum()
@property
def atomic_type(self):
return self.occupation.atomic_type
@cached_property
def atomic_types(self):
"""
This method provides the access to the atomic types of the current site.
Returns
-------
atomic_types: AtomicTypesLookup
Object, that can be indexed either by integer - position in the occupation (ordered) dictionary,
or string - chemical symbol. It returns the atomic type, corresponding to the current position.
"""
class AtomicTypesLookup:
def __getitem__(_self, name):
return self.occupation.atomic_type(name)
def __setitem__(_self, name, value):
return self.occupation.replace_type(name, value)
return AtomicTypesLookup()
[docs]
class Site:
[docs]
@staticmethod
def create(atoms, occupation, reference_system=None, mesh=None):
site_type = SiteType(atoms, occupation, reference_system, mesh)
return Site(site_type)
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@staticmethod
def copy_if_needed(atoms, old_site, site_type):
if not old_site:
return Site(site_type)
if old_site.atoms is not atoms:
return old_site.copy(site_type)
old_site.site_type = site_type
return old_site
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@staticmethod
def copy_sites(sites, atoms=False):
cache = {}
def site(x):
st = x._site_type
n_st = cache.get(st, None)
if not n_st:
cache[st] = n_st = st.copy(atoms=False)
return x.copy(site_type = n_st)
try:
return np.fromiter((site(i) for i in sites), dtype=object, count=len(sites))
except ValueError: # python 3.7 compatibility (or some old numpy version?)
out = np.empty_like(sites)
for i,s in enumerate(sites):
out[i] = s
return out
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def __init__(self, site_type):
assert isinstance(site_type, SiteType)
self._site_type = None
self.site_type = site_type
def __del__(self):
if self._site_type:
self._site_type.unregister(self)
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def unregister(self):
if self._site_type:
self._site_type.unregister(self)
self._site_type = None
@property
def site_type(self):
return self._site_type
@site_type.setter
def site_type(self, site_type):
if self._site_type:
self._site_type.unregister(self)
self._site_type = site_type
if site_type:
self._site_type.register(self)
@property
def has_symmetry(self):
return self._site_type.has_symmetry
[docs]
def break_symmetry(self):
if self.has_symmetry:
self.site_type = self.site_type.copy()
@property
def mesh(self):
return self._site_type.mesh
@mesh.setter
def mesh(self, mesh):
self._site_type.mesh = mesh
[docs]
def remesh(self, mesh, map=None):
return self._site_type.remesh(mesh, map)
@property
def potential(self):
return self._site_type.potential
@potential.setter
def potential(self, potential):
self._site_type.potential = potential
@property
def charge(self):
return self._site_type.charge
@charge.setter
def charge(self, charge):
self._site_type.charge = charge
@property
def moments(self):
return self._site_type.moments
@moments.setter
def moments(self, moments):
self._site_type.moments = moments
@property
def occupation(self):
return self._site_type.occupation
@occupation.setter
def occupation(self, occupation):
self._site_type.occupation = occupation
@property
def reference_system(self):
return self._site_type.reference_system
@reference_system.setter
def reference_system(self, reference_system):
self._site_type.reference_system = reference_system
@property
def primary_symbol(self):
""" Symbol of the most important (most probable) chemical element present on the site. """
return self._site_type.primary_symbol
@property
def primary_atomic_number(self):
""" Atomic symbol of the most important (most probable) chemical element present on the site. """
return self._site_type.primary_atomic_number
@property
def is_vacuum(self):
return self._site_type.is_vacuum
def __str__(self):
return f"Site:{self.occupation}"
def __repr__(self):
return f"Site:{self.occupation}"
@property
def atoms(self):
return self._site_type.atoms
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def copy(self, site_type: Optional[Union[bool,SiteType]]=False):
"""
Copy the site, optionally setting the new site_type (possibly to None) or
copy the exiting one.
"""
out = copy.copy(self)
if site_type:
if not isinstance(site_type, SiteType):
site_type = out._site_type.copy()
if site_type is not False:
out._site_type = site_type
if out._site_type:
out._site_type.register(out)
return out
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def _clear_data(self):
return self._site_type._clear_data()
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def reset(self):
return self._site_type.reset()
@property
def atomic_type(self):
return self.site_type.atomic_type
@cached_property
def atomic_types(self):
return self.site_type.atomic_types
from .occupations import Occupation # NOQA: E402