[Pw_forum] Conserving the same Wyckoff multiplicity in the input and in the output
stefano de gironcoli
degironc at sissa.it
Wed Apr 19 16:48:10 CEST 2017
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
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>>>>>>> _______________________________________________
>>>>>>> Pw_forum mailing list
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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
>>>> _______________________________________________
>>>> 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
>>>
>
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