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
