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Structure.py
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# coding=utf8
'''
Created on
@author: hebing
'''
import re
import numpy as np
import ase.spacegroup as spg
from scipy.spatial.ckdtree import cKDTree
#from pymatgen.core.periodic_table import Element
class Site(object):
'''
'''
def __init__(self,sitelabel=[],Pos=None,elementsoccupy=None):
self._Id=0
self._SiteLabel=sitelabel
self._SiteType=[]
self._FracPostion=Pos
self._Elements_occupy={}
self._Elements_OxiValue={}
self.SetElementsOccupy(elementsoccupy)
def SetSiteType(self,sitetype):
if sitetype not in self._SiteType:
self._SiteType.append(sitetype)
def GetSiteType(self):
return self._SiteType
def SetSiteLabel(self,sitelabel):
if sitelabel != self._SiteLabel:
self._SiteLabel=self._SiteLabel+sitelabel
def SetPostion(self,pos=None):
self._FracPostion=pos
def SetElementsOccupy(self,eleocu):
for key in eleocu.keys():
if key in self._Elements_occupy:
pass#self._Elements_occupy[key]=self._Elements_occupy[key]+eleocu[key]
else:
self._Elements_occupy[key]=eleocu[key]
def SetElementsOxiValue(self,eleoxi):
for key in eleoxi.keys():
self._Elements_OxiValue[key]=eleoxi[key]
def GetElementsOxiValue(self):
return self._Elements_OxiValue
def SetSiteId(self,siteid=0):
self._Id=siteid
def GetSiteId(self):
return self._Id;
def GetSiteLabel(self):
return self._SiteLabel
def GetPosition(self):
return self._FracPostion
def GetElementsOccupy(self ):
return self._Elements_occupy
def GetElements(self):
return self._Elements_occupy.keys()
def GetIronType(self):
for (key,value) in self._Elements_OxiValue.items():
if value<0:
return -1
elif value>0:
return 1
else:
return 0
return 0
class PeriodSite(Site):
def __init__(self,parent=None,sitelabel=[],sitetype=None,Pos=None,elementsoccupy=None):
super(PeriodSite,self).__init__(sitelabel,sitetype,Pos, elementsoccupy)
self.__ParentStruct=parent
self.__ExpandCell=np.array([[0,0,0],[0,0,0]])
def SetParentStructure(self,parent):
self.__ParentStruct=parent
def GetExpandCell(self):
return self.__ExpandCell
class Bond(object):
def __init__(self,site0=None,site1=None,startpos=[0,0,0],endpos=[0,0,0]):
self._Site0=site0
self._Site1=site1
self._Positions = [startpos, endpos]
def get_postions(self):
return self._Positions
def set_postions(self, value):
self._Positions = value
def del_postions(self):
del self._Positions
def get_site_0(self):
return self._Site0
def get_site_1(self):
return self._Site1
def set_site_0(self, value):
self._Site0 = value
def set_site_1(self, value):
self._Site1 = value
def del_site_0(self):
del self._Site0
def del_site_1(self):
del self._Site1
def SetSites(self,site0=None,site1=None):
self._Site0=site0
self._Site1=site1
Site0 = property(get_site_0, set_site_0, del_site_0, "Site0's docstring")
Site1 = property(get_site_1, set_site_1, del_site_1, "Site1's docstring")
Positions = property(get_postions, set_postions, del_postions, "Postions's docstring")
class Polyhedra(object):
def __init__(self):
self._VertexSites=[]
self._CentreSite=None
self._VertexVectors=[]
def get_vertex_vectors(self):
return self._VertexVectors
def set_vertex_vectors(self, value):
self._VertexVectors = value
def del_vertex_vectors(self):
del self._VertexVectors
def get_centre_site(self):
return self._CentreSite
def set_centre_site(self, value):
self._CentreSite = value
def del_centre_site(self):
del self._CentreSite
def get_sites(self):
return self._VertexSites
def set_sites(self, value):
self._VertexSites = value
def del_sites(self):
del self._VertexSites[:]
def get_label(self):
return self._CentreSite.GetSiteLabel()
Label = property(get_label)
VertexSites = property(get_sites, set_sites, del_sites, "Sites's docstring")
CentreSite = property(get_centre_site, set_centre_site, del_centre_site, "CentreSites's docstring")
VertexVectors = property(get_vertex_vectors, set_vertex_vectors, del_vertex_vectors, "VertexVectors's docstring")
class Structure(object):
def __init__(self):
self.__abc=[]
self.__alphabetagama=[]
self.__positions=[]
self._initsites=[]
self._Sites=[]
self._SuperCellusites=[]
self._SuperCellusitesFracPos=[]
self._SuperCellusitesCartPos=[]
self.__SuperCellusitesCellIndex=[]
self.__spacegroupno=1
self.__ABC=[]
self.__equivviewsites=[]
self.__KDtree=None
# self.__ElementsSymbol={}
self._Polyhedras={}
self._Bonds={}
self.__usitepos=[]
self._OxidationTable={}
self._atomsymbols=[]
def get_atomsymbols(self):
return self._atomsymbols
def get_polyhedras(self):
return self._Polyhedras
def set_polyhedras(self, value):
self._Polyhedras = value
def del_polyhedras(self):
del self._Polyhedras
def get_bonds(self):
return self._Bonds
def set_bonds(self, value):
self._Bonds = value
def del_bonds(self):
del self._Bonds
def Setabc(self,abc):
self.__abc=abc
def Getabc(self):
return self.__abc
def SetABC(self,ABC=None):
self.__ABC=ABC
def GetABC(self):
return self.__ABC
def GetSuperCellusitesFracPos(self):
return self._SuperCellusitesFracPos
def GetSuperCellusites(self):
return self._SuperCellusites
def GetSuperCellusitesCartPos(self):
return self._SuperCellusitesCartPos
def ExpandCell(self):
indexpos=[-2.0,-1.0,0.0,1.0,2.0]
del self._SuperCellusites[:]
del self._SuperCellusitesFracPos[:]
del self._SuperCellusitesCartPos[:]
for k in range(5):
for j in range(5):
for i in range(5):
for ste in self._Sites:
pos=ste.GetPosition()
stepos=[pos[0]+indexpos[i],pos[1]+indexpos[j],pos[2]+indexpos[k]]
self._SuperCellusitesFracPos.append(stepos.copy())
cartpos=self.FracPosToCartPos(stepos)
self._SuperCellusitesCartPos.append(cartpos.copy())
self._SuperCellusites.append(ste)
self.__KDtree=cKDTree(self._SuperCellusitesCartPos)
def GetNeighbors(self,centre,r):
return self.__KDtree.query_ball_point(centre, r)
def GetKNeighbors(self,centre,kn):
return self.__KDtree.query(centre, kn,p=2,n_jobs=-1)
def FracPosToCartPos(self,FracPos):
#pos=self.__ABC[0]*FracPos[0]+self.__ABC[1]*FracPos[1]+self.__ABC[2]*FracPos[2]
pos=np.dot(FracPos,self.__ABC)
return pos
def CreateBonds(self,r):
self._Bonds.clear()
for ste in self._Sites:
if ste.GetIronType()>0:
stepos=ste.GetPosition()
cartpos=self.FracPosToCartPos(stepos)
# neighbors=self.GetKNeighbors(cartpos, r=3)
(distance,neighbors)=self.GetKNeighbors(cartpos, kn=12)
if len(neighbors)>1:
polyhedra=Polyhedra()
polyhedra.CentreSite=ste
for (i,index) in enumerate(neighbors[1:]):
site2=self._SuperCellusites[index]
fracpos2=self._SuperCellusitesFracPos[index]
if site2.GetIronType()<0 and distance[i+1]<r:
bond=Bond(ste,site2)
bond.Positions=[stepos,fracpos2]
if not ste.GetSiteId() in self._Bonds:
self._Bonds[ste.GetSiteId()]=[]
self._Bonds[ste.GetSiteId()].append(bond)
polyhedra.VertexSites.append(site2)
polyhedra.VertexVectors.append(fracpos2-stepos)
else:
break
self._Polyhedras[ste.GetSiteId()]=polyhedra
def CreateAllBonds(self):
self.CreateBonds(r=3)
def SetSpaceGroupno(self,spacegroupid=1):
self.__spacegroupno=spacegroupid
def GetSpaceGroupno(self):
return self.__spacegroupno
def SetAlphaBetaGama(self,abg):
self.__alphabetagama=abg
def GetAlphaBetaGama(self):
return self.__alphabetagama
def AddSite(self,site=None):
self._initsites.append(site)
def GetSites(self):
return self._initsites
def GetUSites(self):
return self._Sites
def GetAseStructure(self,atoms=None):
self.Setabc([atoms.info['_cell_length_a'],atoms.info['_cell_length_b'],atoms.info['_cell_length_c']])
self.SetAlphaBetaGama([atoms.info['_cell_angle_alpha'],atoms.info['_cell_angle_beta'],atoms.info['_cell_angle_gamma']])
if '_symmetry_int_tables_number' in atoms.info:
self.SetSpaceGroupno( atoms.info['_symmetry_int_tables_number' ])
elif '_space_group_it_number' in atoms.info:
self.SetSpaceGroupno( atoms.info['_space_group_it_number' ])
else:
print('can not find group no')
return
index=0
self.__ABC=atoms.cell
postions=list(zip(atoms.info['_atom_site_fract_x'],atoms.info['_atom_site_fract_y'],atoms.info['_atom_site_fract_z']))
no = None
if '_space_group.it_number' in atoms.info:
no = atoms.info['_space_group.it_number']
elif '_space_group_it_number' in atoms.info:
no = atoms.info['_space_group_it_number']
elif '_symmetry_int_tables_number' in atoms.info:
no = atoms.info['_symmetry_int_tables_number']
symbolHM = None
if '_space_group.Patterson_name_h-m' in atoms.info:
symbolHM = atoms.info['_space_group.patterson_name_h-m']
elif '_symmetry_space_group_name_h-m' in atoms.info:
symbolHM = atoms.info['_symmetry_space_group_name_h-m']
elif '_space_group_name_h-m_alt' in atoms.info:
symbolHM = atoms.info['_space_group_name_h-m_alt']
sitesym = None
for name in ['_space_group_symop_operation_xyz',
'_space_group_symop.operation_xyz',
'_symmetry_equiv_pos_as_xyz']:
if name in atoms.info:
sitesym = atoms.info[name]
break
else:
sitesym = None
spgroup = 1
if sitesym is not None:
# subtrans = [(0.0, 0.0, 0.0)]
# spgroup = spg.spacegroup.spacegroup_from_data(no=no, symbol=symbolHM, sitesym=sitesym, subtrans=subtrans)
spgroup=spg.Spacegroup(self.GetSpaceGroupno())
# spgroup=spg.Spacegroup(self.GetSpaceGroupno())
kinds=[]
ssites,kinds=spgroup.equivalent_sites(postions,onduplicates='keep')
self.__positions=ssites
if '_atom_type_oxidation_number' in atoms.info:
for i,atomtype in enumerate(atoms.info['_atom_type_symbol']):
self._OxidationTable[atomtype]=int(atoms.info['_atom_type_oxidation_number'][i])
atomsymbols=set([])
for ssite in ssites:
s=atoms.info['_atom_site_type_symbol'][kinds[index]]
m = re.search(r'([A-Z][a-z]?)', s)
symbol = m.group(0)
atomsymbols.add(symbol)
stelabel=atoms.info['_atom_site_label'][kinds[index]]
eleoccupy={symbol:atoms.info['_atom_site_occupancy'][kinds[index]]}
self.AddSite(Site(sitelabel=stelabel,Pos=ssite,elementsoccupy=eleoccupy))
self._initsites[index].SetSiteType(s)
self._initsites[index].SetSiteId(index)
if len(self._OxidationTable) >0:
eleoxi={symbol:self._OxidationTable[s]}
self._initsites[index].SetElementsOxiValue(eleoxi)
index=index+1
self._atomsymbols=[i for i in atomsymbols]
self.MergeDuplicateSite(0.001)
self.ExpandCell()
self.CreateAllBonds()
def MergeDuplicateSite(self,symprec=0.001):
dupsites=[False]*len(self.__positions)
sitelabels=[]
for index,sitepos in enumerate(self.__positions):
if not dupsites[index]:
self.__usitepos.append(self.__positions[index])
#_site=Site(sitelabel=self._initsites[index].GetSiteLabel(),Pos=sitepos,elementsoccupy=self._initsites[index].GetElementsOccupy())
self._Sites.append(self._initsites[index])
sitelabels.append([self._initsites[index].GetSiteLabel()])
self._Sites[-1].SetSiteId(len(self._Sites)-1)
t = sitepos - self.__positions
mask = np.all((abs(t) < symprec) |(abs(abs(t) - 1.0) < symprec), axis=1)
if np.any(mask):
inds = np.argwhere(mask).tolist()
if len(inds)>1:
for dindex in inds:
dupsites[dindex[0]]=True
_occupy=self._initsites[dindex[0]].GetElementsOccupy()
_sitelabel=self._initsites[dindex[0]].GetSiteLabel()
_sitetype=self._initsites[dindex[0]].GetSiteType()
if index !=dindex[0] and (not _sitelabel in sitelabels[-1] ):
sitelabels[-1].append(_sitelabel)
for stype in _sitetype:
# print(index)
self._Sites[-1].SetSiteType(stype)
m = re.search(r'([A-Z][a-z]?)', stype)
symbol = m.group(0)
if len(self._OxidationTable) >0:
eleoxi={symbol:self._OxidationTable[stype]}
self._Sites[-1].SetElementsOxiValue(eleoxi)
self._Sites[-1].SetElementsOccupy(_occupy)
self._Sites[-1].SetSiteLabel(_sitelabel)
Bonds = property(get_bonds, set_bonds, del_bonds, "Bonds's docstring")
Polyhedras = property(get_polyhedras, set_polyhedras, del_polyhedras, "Polyhedras's docstring")