[QE-users] Symmetry identification difference between QE versions

Shimin Zhang szhan213 at ucsc.edu
Sat Feb 11 00:17:31 CET 2023


Dear all,
I'm calculating a hBN defect in a supercell. This defect system is supposed
to be D3h symmetry. I did several tests and found the symmetry is
identified differently when I use different versions and different sizes of
supercell. Here's the test i did:

In one defect system (removing one Nitrogen from the supercell, symmetry
was expected to be D3h):
1. QE 7.1 version and 6x6 supercell, cell coordinate set by  iibrav =
0. system is able to identify D3h.
      isym =  1     identity


 cryst.   s( 1) = (     1          0          0      )

                  (     0          1          0      )

                  (     0          0          1      )


 cart.    s( 1) = (  1.0000000  0.0000000  0.0000000 )

                  (  0.0000000  1.0000000  0.0000000 )

                  (  0.0000000  0.0000000  1.0000000 )



      isym =  2     180 deg rotation - cart. axis [0,1,0]


 cryst.   s( 2) = (    -1          0          0      )    f =(  0.3333323 )

                  (     1          1          0      )       (  0.0000000 )

                  (     0          0         -1      )       (  0.0000000 )


 cart.    s( 2) = ( -1.0000000 -0.0000003  0.0000000 )    f =(  0.3333323 )

                  (  0.0000000  1.0000000  0.0000000 )       (  0.0000000 )

                  (  0.0000000  0.0000000 -1.0000000 )       (  0.0000000 )



      isym =  3     120 deg rotation - cryst. axis [0,0,1]


 cryst.   s( 3) = (     0          1          0      )    f =( -0.0000004 )

                  (    -1         -1          0      )       ( -0.3333327 )

                  (     0          0          1      )       (  0.0000000 )


 cart.    s( 3) = ( -0.5000001 -0.8660255  0.0000000 )    f =(  0.1666660 )

                  (  0.8660253 -0.4999999  0.0000000 )       ( -0.2886745 )

                  (  0.0000000  0.0000000  1.0000000 )       (  0.0000000 )



      isym =  4     120 deg rotation - cryst. axis [0,0,-1]


 cryst.   s( 4) = (    -1         -1          0      )    f =(  0.3333324 )

                  (     1          0          0      )       ( -0.0000003 )

                  (     0          0          1      )       (  0.0000000 )


 cart.    s( 4) = ( -0.4999999  0.8660255  0.0000000 )    f =(  0.3333325 )

                  ( -0.8660253 -0.5000001  0.0000000 )       ( -0.0000003 )

                  (  0.0000000  0.0000000  1.0000000 )       (  0.0000000 )


      isym =  5     180 deg rotation - cryst. axis [1,-1,0]


 cryst.   s( 5) = (     0         -1          0      )

                  (    -1          0          0      )

                  (     0          0         -1      )


 cart.    s( 5) = (  0.5000001 -0.8660253  0.0000000 )

                  ( -0.8660253 -0.5000001  0.0000000 )

                  (  0.0000000  0.0000000 -1.0000000 )



      isym =  6     180 deg rotation - cryst. axis [2,1,0]


 cryst.   s( 6) = (     1          1          0      )    f =( -0.0000000 )

                  (     0         -1          0      )       ( -0.3333327 )

                  (     0          0         -1      )       (  0.0000000 )


 cart.    s( 6) = (  0.4999999  0.8660256  0.0000000 )    f =(  0.1666664 )

                  (  0.8660253 -0.4999999  0.0000000 )       ( -0.2886745 )

                  (  0.0000000  0.0000000 -1.0000000 )       (  0.0000000 )



      isym =  7     inv. 180 deg rotation - cart. axis [0,0,1]


 cryst.   s( 7) = (     1          0          0      )

                  (     0          1          0      )

                  (     0          0         -1      )


 cart.    s( 7) = (  1.0000000  0.0000000  0.0000000 )

                  (  0.0000000  1.0000000  0.0000000 )

                  (  0.0000000  0.0000000 -1.0000000 )



      isym =  8     inv. 180 deg rotation - cart. axis [1,0,0]


 cryst.   s( 8) = (    -1          0          0      )    f =(  0.3333323 )

                  (     1          1          0      )       (  0.0000000 )

                  (     0          0          1      )       (  0.0000000 )


 cart.    s( 8) = ( -1.0000000 -0.0000003  0.0000000 )    f =(  0.3333323 )

                  (  0.0000000  1.0000000  0.0000000 )       (  0.0000000 )

                  (  0.0000000  0.0000000  1.0000000 )       (  0.0000000 )

      isym =  9     inv.  60 deg rotation - cryst. axis [0,0,1]


 cryst.   s( 9) = (    -1         -1          0      )    f =(  0.3333324 )

                  (     1          0          0      )       ( -0.0000003 )

                  (     0          0         -1      )       (  0.0000000 )


 cart.    s( 9) = ( -0.4999999  0.8660255  0.0000000 )    f =(  0.3333325 )

                  ( -0.8660253 -0.5000001  0.0000000 )       ( -0.0000003 )

                  (  0.0000000  0.0000000 -1.0000000 )       (  0.0000000 )



      isym = 10     inv.  60 deg rotation - cryst. axis [0,0,-1]


 cryst.   s(10) = (     0          1          0      )    f =( -0.0000004 )

                  (    -1         -1          0      )       ( -0.3333327 )

                  (     0          0         -1      )       (  0.0000000 )


 cart.    s(10) = ( -0.5000001 -0.8660255  0.0000000 )    f =(  0.1666660 )

                  (  0.8660253 -0.4999999  0.0000000 )       ( -0.2886745 )

                  (  0.0000000  0.0000000 -1.0000000 )       (  0.0000000 )



      isym = 11     inv. 180 deg rotation - cryst. axis [0,1,0]


 cryst.   s(11) = (     1          1          0      )    f =( -0.0000000 )

                  (     0         -1          0      )       ( -0.3333327 )

                  (     0          0          1      )       (  0.0000000 )


 cart.    s(11) = (  0.4999999  0.8660256  0.0000000 )    f =(  0.1666664 )

                  (  0.8660253 -0.4999999  0.0000000 )       ( -0.2886745 )

                  (  0.0000000  0.0000000  1.0000000 )       (  0.0000000 )



      isym = 12     inv. 180 deg rotation - cryst. axis [1,1,0]


 cryst.   s(12) = (     0         -1          0      )

                  (    -1          0          0      )

                  (     0          0          1      )


 cart.    s(12) = (  0.5000001 -0.8660253  0.0000000 )

                  ( -0.8660253 -0.5000001  0.0000000 )

                  (  0.0000000  0.0000000  1.0000000 )


2. QE 7.1 version and 8x8 supercell, cell coordinate set by iibrav = 0,
system only detected 4 symmetry operator (C2v)

      4 Sym. Ops. (no inversion) found



                                    s                        frac. trans.


      isym =  1     identity


 cryst.   s( 1) = (     1          0          0      )

                  (     0          1          0      )

                  (     0          0          1      )


 cart.    s( 1) = (  1.0000000  0.0000000  0.0000000 )

                  (  0.0000000  1.0000000  0.0000000 )

                  (  0.0000000  0.0000000  1.0000000 )



      isym =  2     180 deg rotation - cryst. axis [1,-1,0]


 cryst.   s( 2) = (     0         -1          0      )

                  (    -1          0          0      )

                  (     0          0         -1      )


 cart.    s( 2) = (  0.5000000 -0.8660254  0.0000000 )

                  ( -0.8660254 -0.5000000  0.0000000 )

                  (  0.0000000  0.0000000 -1.0000000 )



      isym =  3     inv. 180 deg rotation - cart. axis [0,0,1]


 cryst.   s( 3) = (     1          0          0      )

                  (     0          1          0      )

                  (     0          0         -1      )


 cart.    s( 3) = (  1.0000000  0.0000000  0.0000000 )

                  (  0.0000000  1.0000000  0.0000000 )

                  (  0.0000000  0.0000000 -1.0000000 )



      isym =  4     inv. 180 deg rotation - cryst. axis [1,1,0]


 cryst.   s( 4) = (     0         -1          0      )

                  (    -1          0          0      )

                  (     0          0          1      )


 cart.    s( 4) = (  0.5000000 -0.8660254  0.0000000 )

                  ( -0.8660254 -0.5000000  0.0000000 )

                  (  0.0000000  0.0000000  1.0000000 )



In another defect system (removing one Boron from the supercell, symmetry
was expected to be D3h):
1. in QE 7.1 version and 6x6 supercell, cell coordinate set by ibrav =0
system, no symmetry found.
2. in QE 7.1 version and 8x8 supercell, cell coordinate set by ibrav =0
system. no symmetry found.
2. in QE 7.1 version and 8x8 supercell, cell coordinate set by ibrav =4
system C2v symmetry found
2. in QE 6.4 version and 8x8 supercell, cell coordinate set by ibrav =4
system D3h symmetry found

basically from the above test i find the symmetry identification is
pretty arbitrary and changed by version and supercell size. I don't know
how the larger supercell size could be wrong if the smaller one is fine,
because I use the same single unit cell to span into different sizes of
supercell.

I tried to reduce the accep in PW/src/symm_base.f90  to 1.0d-3 to reduce
the sensitivity of symmetry identification, but it doesn't help.

My question is what could be the factor to cause this arbitrary symmetry
identification?
What is the difference between these two versions of QE in the sense of
identifying the symmetry?
What is the consequence if some symmetry operators are missed?
Can I input the symmetry myself?

Best,
Shimin Zhang
PhD student  in University of California, Santa Cruz
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