sisl.Geometry
=============















.. currentmodule:: sisl

.. autoclass:: Geometry







   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         


   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         

   
      
         
      
         
      
         
      
         
            

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
      
         
      
         
      

   
      
         
            
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
      

   
      
      
         
      
         
            
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      

   
      
      
         
      
      







   .. rubric:: Conversion

   .. autosummary::
      :removeprefix: Geometry.

      
      Geometry.new
      
      





   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   


   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   
      
      Geometry.new.Sile

   
      
      Geometry.new.ase

   
      
      Geometry.new.pymatgen

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   
      
      Geometry.to
      
      





   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   


   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   
      
      Geometry.to.Path

   
      
      Geometry.to.Sile

   
      
      Geometry.to.ase

   
      
      Geometry.to.dataframe

   
      
      Geometry.to.pymatgen

   
      
      Geometry.to.str

   

   

   

   

   

   

   

   

   




   .. rubric:: Plotting

   .. autosummary::
      :removeprefix: Geometry.

      Geometry.plot
      





   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   


   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   
      
      Geometry.plot.geometry

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   

   








   .. rubric:: Methods

   .. autosummary::
      





   

   

   
   
      
      

   
      
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.Rij

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.a2isc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.a2o

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.a2sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.a2transpose

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.add

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.add_vacuum

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.angle

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.append

   

   

   
   
      
      

   
      
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.area

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.as_primary

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.as_supercell

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.asc2uc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.attach

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.auc2sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.axyz

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.bond_correct

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.center

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.close

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.close_sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.copy

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.dihedral

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.distance

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.equal

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.find_nsc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iR

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.insert

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter_block

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter_block_rand

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter_block_shape

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter_orbitals

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.iter_species

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.maxR

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.mirror

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.move

   

   

   
   

   
      
      
      
      
         

   

   

   

   
   

   
      
      
      
      
         

   

   

   

   
   

   
      
      
      
      
         

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.o2a

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.o2isc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.o2sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.o2transpose

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.oRij

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.optimize_nsc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.orij

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.osc2uc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.ouc2sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.overlap

   

   

   
   

   
      
         
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.prepend

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.read

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.reduce

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.remove

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.remove_orbital

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.reorder

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.repeat

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.replace

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.reverse

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.rij

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.rotate

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.rotate_miller

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sc2uc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sc_index

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.scale

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.set_lattice

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.set_nsc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.set_supercell

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sort

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sparserij

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sub

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sub_orbital

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.swap

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.swapaxes

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.tile

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
         
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.translate

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.translate2uc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.uc2sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.unrepeat

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.untile

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.within

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.within_inf

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.within_sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.write




   .. rubric:: Attributes

   .. autosummary::
      





   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.atoms

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.boundary_condition

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.cell

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.firsto

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.fxyz

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.icell

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.isc_off

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.lasto

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.length

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.mass

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.n_s

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.na

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.na_s

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.names

   

   

   
   
      
      

   
      
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.no

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.no_s

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.nsc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.orbitals

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.origin

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.pbc

   

   

   
   
      
      

   
      
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.q0

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.rcell

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sc

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.sc_off

   

   

   
   
      
      

   
      
      
      
      

   

   

   

   
   

   
      
      
      
      

   
      
   
      ~Geometry.volume