[Pw_forum] Conserving the same Wyckoff multiplicity in the input and in the output
Paolo Giannozzi
p.giannozzi at gmail.com
Wed Apr 12 12:36:16 CEST 2017
The symmetry the code finds may differ from the actual symmetry of the
system. If so, only a reduced symmetry will be enforced. Note the last
point in this excerpt from the user manual. It holds also for Wyckoff
positions and space groups.
Paolo
===========================================
5.0.0.19 pw.x does not find all the symmetries you expected
pw.x determines first the symmetry operations (rotations) of the
Bravais lattice; then checks which of these are symmetry operations of
the system (including if needed fractional translations). This is done
by rotating (and translating if needed) the atoms in the unit cell and
verifying if the rotated unit cell coincides with the original one.
Assuming that your coordinates are correct (please carefully check!),
you may not find all the symmetries you expect because:
the number of significant figures in the atomic positions is not large
enough. In file PW/eqvect.f90, the variable accep is used to decide
whether a rotation is a symmetry operation. Its current value (10-5 )
is quite strict: a rotated atom must coincide with another atom to 5
significant digits. You may change the value of accep and recompile.
they are not acceptable symmetry operations of the Bravais lattice.
This is the case for C60 , for instance: the Ih icosahedral group of
C60 contains 5-fold rotations that are incompatible with translation
symmetry.
the system is rotated with respect to symmetry axis. For instance: a
C60 molecule in the fcc lattice will have 24 symmetry operations (Th
group) only if the double bond is aligned along one of the crystal
axis; if C60 is rotated in some arbitrary way, pw.x may not find any
symmetry, apart from inversion.
they contain a fractional translation that is incompatible with the
FFT grid (see next paragraph). Note that if you change cutoff or unit
cell volume, the automatically computed FFT grid changes, and this may
explain changes in symmetry (and in the number of k-points as a
consequence) for no apparent good reason (only if you have fractional
translations in the system, though).
a fractional translation, without rotation, is a symmetry operation of
the system. This means that the cell is actually a supercell. In this
case, all symmetry operations containing fractional translations are
disabled. The reason is that in this rather exotic case there is no
simple way to select those symmetry operations forming a true group,
in the mathematical sense of the term.
5.0.0.20 Warning: symmetry operation # N not allowed
This is not an error. If a symmetry operation contains a fractional
translation that is incompatible with the FFT grid, it is discarded in
order to prevent problems with symmetrization. Typical fractional
translations are 1/2 or 1/3 of a lattice vector. If the FFT grid
dimension along that direction is not divisible respectively by 2 or
by 3, the symmetry operation will not transform the FFT grid into
itself. Solution: you can either force your FFT grid to be
commensurate with fractional translation (set variables nr1, nr2, nr3
to suitable values), or set variable use_all_frac to .true., in
namelist &SYSTEM. Note however that the latter is incompatible with
hybrid functionals and with phonon calculations.
===========================================
On Wed, Apr 12, 2017 at 12:03 PM, hqtst42 <hqtst42 at netc.pl> wrote:
> Hi Paolo,
>
> Many thanks for your reply ; maybe the problem may be something
> different ; I see a symmetry break from the gipaw simulation. Because of
> the symmetry, I expect, for example, 4 carbons with identical chemical
> shifts, yet I have 2 pairs of 2 equivalent carbon instead. For example:
>
> -------------------------------------------------------------------------------------------
>
> Total NMR chemical shifts in ppm:
> ---------------------------------------
> (adopting the Simpson convention for anisotropy and
> asymmetry)-----------
>
> Atom 1 C pos: ( 0.702166 0.334168 0.055776) Total
> sigma: 154.68
> 95.6267 39.1235 -16.2688
> 45.6199 165.6715 -100.3341
> -21.3569 -108.3456 202.7526
>
> C 1 anisotropy: 216.17 eta: -0.2840
> C 1 sigma_11= 103.0939 axis=( 0.761900 0.370231 0.531448)
> C 1 sigma_22= 62.1589 axis=( 0.615219 -0.670233 -0.415082)
> C 1 sigma_33= 298.7979 axis=( -0.202517 -0.643208 0.738424)
>
> Atom 2 C pos: ( 0.297834 0.203502 0.675798) Total
> sigma: 154.68
> 95.6267 39.1235 -16.2688
> 45.6199 165.6715 -100.3341
> -21.3569 -108.3456 202.7526
>
> C 2 anisotropy: 216.17 eta: -0.2840
> C 2 sigma_11= 103.0939 axis=( 0.761900 0.370231 0.531448)
> C 2 sigma_22= 62.1589 axis=( 0.615219 -0.670233 -0.415082)
> C 2 sigma_33= 298.7979 axis=( -0.202517 -0.643208 0.738424)
>
> Atom 3 C pos: ( 0.297163 0.472864 0.419799) Total
> sigma: 155.11
> 95.2156 39.0348 15.4560
> 45.5222 166.0586 99.6009
> 19.2085 107.7438 204.0451
>
> C 3 anisotropy: 215.17 eta: -0.2971
> C 3 sigma_11= 104.6936 axis=( -0.750294 -0.387720 0.535474)
> C 3 sigma_22= 62.0730 axis=( -0.631164 0.661092 -0.405696)
> C 3 sigma_33= 298.5528 axis=( 0.196701 0.642363 0.740729)
>
> Atom 4 C pos: ( 0.702837 0.064806 0.311775) Total
> sigma: 155.11
> 95.2156 39.0348 15.4560
> 45.5222 166.0586 99.6009
> 19.2085 107.7438 204.0451
>
> C 4 anisotropy: 215.17 eta: -0.2971
> C 4 sigma_11= 104.6936 axis=( -0.750294 -0.387720 0.535474)
> C 4 sigma_22= 62.0730 axis=( -0.631164 0.661092 -0.405696)
> C 4 sigma_33= 298.5528 axis=( 0.196701 0.642363 0.740729)
>
> -------------------------------------------------------------------------------------------
>
> There is apparently no version number for
> GIPAW:
>
> -------------------------------------------------------------------------------------------
> Program QE v.6.0 (svn rev. 13079) starts on 16Mar2017 at 19:27:28
> ***** This is GIPAW svn revision unknown *****
> -------------------------------------------------------------------------------------------
>
> Many thanks again for your time.
>
> Henri Colaux
>
>
> Le 2017/04/05 à 15:31, Paolo Giannozzi a écrit :
>> This is what you get:
>> 2 Sym. Ops., with inversion, found
>> (note: 2 additional sym.ops. were found but ignored
>> their fractional translations are incommensurate with FFT grid)
>> and this is what you get if you specify "use_all_frac=.true.":
>> 4 Sym. Ops., with inversion, found ( 2 have fractional translation)
>> These are symmetry operations (visible with verbosity='high')
>> 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 - cart. axis [0,0,1]
>>
>> cryst. s( 2) = ( -1 0 0 ) f =( 0.0000000 )
>> ( 0 -1 0 ) ( 0.5000000 )
>> ( 0 0 1 ) ( 0.5000000 )
>>
>> cart. s( 2) = ( -1.0000000 0.0000000 0.0000000 ) f =( 0.0000000 )
>> ( 0.0000000 -1.0000000 0.0000000 ) ( 0.2688348 )
>> ( 0.0000000 0.0000000 1.0000000 ) ( 0.3657871 )
>>
>>
>> isym = 3 inversion
>>
>> 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 - cart. axis [0,0,1]
>>
>> cryst. s( 4) = ( 1 0 0 ) f =( 0.0000000 )
>> ( 0 1 0 ) ( 0.5000000 )
>> ( 0 0 -1 ) ( 0.5000000 )
>>
>> cart. s( 4) = ( 1.0000000 0.0000000 0.0000000 ) f =( 0.0000000 )
>> ( 0.0000000 1.0000000 0.0000000 ) ( 0.2688348 )
>> ( 0.0000000 0.0000000 -1.0000000 ) ( 0.3657871 )
>>
>>
>> point group C_2h (2/m)
>> there are 4 classes
>> the character table:
>>
>> E C2 i s_h
>> A_g 1.00 1.00 1.00 1.00
>> B_g 1.00 -1.00 1.00 -1.00
>> A_u 1.00 1.00 -1.00 -1.00
>> B_u 1.00 -1.00 -1.00 1.00
>>
>> the symmetry operations in each class and the name of the first element:
>>
>> E 1
>> identity
>> C2 2
>> 180 deg rotation - cart. axis [0,0,1]
>> i 3
>> inversion
>> s_h 4
>> inv. 180 deg rotation - cart. axis [0,0,1]
>>
>> On Wed, Apr 5, 2017 at 7:51 AM, Paolo Giannozzi <p.giannozzi at gmail.com> wrote:
>>> Structural optimization doesn't break the symmetry. The final symmetry
>>> - the one found by the code, I mean - should be the same as the
>>> initial one.
>>>
>>> On Wed, Apr 5, 2017 at 2:46 AM, hqtst42 <hqtst42 at netc.pl> wrote:
>>>> In the input file, there are the atomic coordinates for only one
>>>> molecule, and with the symmetry operation, I expect 4 equivalent
>>>> molecules per unit cell. Yet, the structure optimisation results in 2
>>>> pairs of 2 equivalent molecules per unit cell. I would like to explain
>>>> to the program not to break the symmetry.
>>>>
>>>> Le 2017/04/04 à 21:45, Paolo Giannozzi a écrit :
>>>>> What do you mean by "results with multiplicity 1" and "Wyckoff multiplicity?
>>>>>
>>>>> On Tue, Apr 4, 2017 at 12:08 PM, hqtst42 <hqtst42 at netc.pl> wrote:
>>>>>> Dear everyone,
>>>>>>
>>>>>> In the enclosed input file, I set atomic coordinates of all equivalent atoms
>>>>>> with crystal_sg and the space group.
>>>>>>
>>>>>> This should give results with a multiplicity of 1, but I have instead a
>>>>>> multiplicity of 2 in the output file.
>>>>>> How can I force the program to conserve the Wyckoff multiplicity taken as an
>>>>>> input ?
>>>>>> All in QE v 6.0
>>>>>>
>>>>>> Many thanks in advance,
>>>>>>
>>>>>> Henri Colaux
>>>>>> Research associate
>>>>>> RIKEN Yokohama
>>>>>>
>>>>>> _______________________________________________
>>>>>> Pw_forum mailing list
>>>>>> Pw_forum at pwscf.org
>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>>>
>>>> _______________________________________________
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>>>
>>>
>>> --
>>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>
>
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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