[Pw_forum] Conserving the same Wyckoff multiplicity in the input and in the output
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Apr 20 14:40:23 CEST 2017
You cannot set a different "ibrav" from what the code expects for a
given space group. If you want a structure with unique axis "b"
(ibrav=-12), set uniqueb=.true.; otherwise, you must use ibrav=12.
Both structures (which are not the same, though) have 4 symmetry
operations
Paolo
On Thu, Apr 20, 2017 at 4:35 AM, hqtst42 <hqtst42 at netc.pl> wrote:
> Here is another example in which one of the symmetries is rejected, yet
> I used "use_all_frac=.true." but I still have two symmetry operation
> instead of four. The main difference here is that I used "ibrav = -12"
> instead of "ibrav = +12".
>
> Many thanks in advance,
>
> Henri
>
>
> Le 2017/04/19 à 23:48, stefano de gironcoli a écrit :
>> a way to avoid the rejection of symmetries with fractionary translation
>> without the use_all_frac=.true. flag is to set the nr1,nr2,nr3
>> dimensions in such a way that all fractionary translation are such that
>> they correspond to translation of an integer number of grid points.
>>
>> for instance if the FT in crystal coordinates is (1/3, 1/2, 0) then nr1
>> must be multiple of 3, nr2 multiple of 2, nr3 is not constrained.
>> The nr1,nr2,nr3 choice must fulfill the constraints imposed by all the
>> FT ... and be compatible with the desired ecutwfc/ecutrho... that is
>> larger than the ones that the code would have chosen by default.
>>
>> stefano
>>
>> On 19/04/2017 11:47, hqtst42 wrote:
>>> Dear Paolo,
>>>
>>> Many thanks for you reply. It seems like "use_all_frac=.true. " solved
>>> my problem.
>>> I have one final question: assuming you use one of the options
>>> that would prevent you from using (hybrid functionals / phonon
>>> calculations), how could I change the input parameters (especially
>>> ecutwfc) so all of the symmetry elements are present ?
>>>
>>> Many thanks indeed,
>>>
>>> Henri Colaux
>>>
>>>
>>>
>>> Le 2017/04/19 à 18:46, Henri Colaux a écrit :
>>>> Le 2017/04/12 à 19:36, Paolo Giannozzi a écrit :
>>>>> 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
>>>>>>>>> _______________________________________________
>>>>>>>>> Pw_forum mailing list
>>>>>>>>> Pw_forum at pwscf.org
>>>>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>>>> --
>>>>>>>> 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
>>>>>> _______________________________________________
>>>>>> Pw_forum mailing list
>>>>>> Pw_forum at pwscf.org
>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>> --
>>>>> 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
>>>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>> _______________________________________________
>> 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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