def showcell(self,bondindex=(1,2),plane=(0,1),color='r',offset=None):
'''
Plot the cell structure.
bondindex:
the bondindex-th nearest bonds are plotted. It should be a tuple.
Default is (1,2) - the nearest, and second nearest neightbors.
plane:
project to the specific plane if it is a 3D structre.
Default is (0,1) - 'x-y' plane.
color:
color, default is 'r' -red.
offset:
The offset of the sample cell.
'''
p1,p2=plane
nnnbonds=self.cbonds
if nnnbonds is None or len(nnnbonds)<=1:
warnings.warn('Trivial [email protected], plot on-site terms only.')
bondindex=()
if offset is None:
offset=[2]*self.dimension
for nb in bondindex:
cb=nnnbonds[nb]
cellindex=self.l2index(append(offset,[0]))
show_bonds(cb,start=self.sites[cellindex+cb.atom1s])
#plot sites
if self.vdim>1:
p1,p2=plane
x,y=self.sites[:,p1],self.sites[:,p2]
else:
x=self.sites[:,0]
y=zeros(self.N)
scatter(x,y,s=50,c=color,edgecolor='none',vmin=-0.5,vmax=1.5)
def show_bonds(self, nth=(1,), plane=(0, 1), color="r"):
"""
Plot the structure.
plane:
project to the specific plane if it is a 3D structre.
Default is (0,1) - 'x-y' plane.
nth:
the n-th nearest bonds are plotted. It should be a tuple.
Default is (1,) - the nearest neightbor.
c:
color, default is 'r' -red.
"""
nnnbonds = self.__nnnbonds__
if nnnbonds is None or len(nnnbonds) <= 1:
warnings.warn("Trivial bonds @Structure.show_bond, give up.")
return
for nb in nth:
bs = nnnbonds[nb]
show_bonds(bs, start=self.sites[bs.atom1s])
