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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >>>>>>> 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 <[email protected]> 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 <[email protected]> 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 >>>>>>>>>>> [email protected] >>>>>>>>>>> http://pwscf.org/mailman/listinfo/pw_forum >>>>>>>>> _______________________________________________ >>>>>>>>> Pw_forum mailing list >>>>>>>>> [email protected] >>>>>>>>> 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 >>>>>> [email protected] >>>>>> 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 >>> [email protected] >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > [email protected] > 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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