[QE-users] problem with number of atoms in pw.x
Paolo Giannozzi
p.giannozzi at gmail.com
Fri Sep 11 14:47:19 CEST 2020
Hi
just guessing: the space-group machinery takes the provided Wyckoff
positions, applies crystal symmetries, throws out translationally
equivalent positions. It works also if positions are provided in the form
(x,y,z) (wrt crystal axis), but you have to ensure that the Wyckoff site
symmetry is correct. I suspect that one or more of the Ge positions are not
exact Wyckoff positions but very close to them.
Paolo
On Fri, Sep 11, 2020 at 2:25 PM José Carlos Conesa Cegarra <
jcconesa at icp.csic.es> wrote:
> Dear all,
>
> I have found a problem with the number of atoms resulting in a
> computation with pw.x. The essentials of the geometry specification are:
>
> &SYSTEM
> space_group=155, rhombohedral=.TRUE.
> A=8.7018, B=8.7018, C=8.7018
> cosAB=-0.0032742, cosAC=-0.0032742, cosBC=-0.0032742
> nat=13, ntyp=4
> ...
>
> /
>
> ATOMIC_POSITIONS crystal_sg
> V 0.00000 0.00000 0.00000
> Ge -0.75399 -0.99800 -0.74920
> N -0.73084 -0.51728 -0.00123
> N -0.01635 -0.01149 -0.23613
> N -0.52047 -0.23372 -0.50080
> N -0.22951 -0.73368 -0.74864
> N -0.26226 -0.48504 -0.98625
> Sn -0.12491 -0.62544 -0.12283
> Ge 0.00000 -0.49511 -0.50488
> Ge -0.50000 -0.75534 -0.24466
> Sn -0.50000 -0.24993 -0.75007
> N -0.76700 -0.76700 -0.76700
> Sn -0.62767 -0.62767 -0.62767
>
> With this input I expect to have 56 atoms, as corresponds to a V-doped
> (Ge,Sn) spinel nitride having almost the same number of Ge and Sn atoms
> (in fact, there is one Sn atom less) as I have verified independently.
> However, I obtain at the beginning of the pw.x calculation the following
> list of atoms:
>
> site n. atom positions (alat units)
> 1 V tau( 1) = ( 0.0000000 0.0000000 0.0000000
> )
> 2 Ge tau( 2) = ( -0.0033926 -0.2015179 0.2870436
> )
> 3 Ge tau( 3) = ( 0.1762159 0.0978209 0.2870436
> )
> 4 Ge tau( 4) = ( -0.1728234 0.1036970 0.2870436
> )
> 5 Ge tau( 5) = ( -0.0033926 0.2015179 1.4393268
> )
> 6 Ge tau( 6) = ( 0.1762159 -0.0978209 1.4393268
> )
> 7 Ge tau( 7) = ( -0.1728234 -0.1036970 1.4393268
> )
> 8 N tau( 8) = ( -0.5167561 -0.1236930 1.0074235
> )
> 9 N tau( 9) = ( 0.3654993 -0.3856774 1.0074235
> )
> 10 N tau( 10) = ( 0.1512567 0.5093704 1.0074235
> )
> 11 N tau( 11) = ( -0.5167561 0.1236930 0.7189470
> )
> 12 N tau( 12) = ( 0.3654993 0.3856774 0.7189470
> )
> 13 N tau( 13) = ( 0.1512567 -0.5093704 0.7189470
> )
> 14 N tau( 14) = ( 0.1556621 0.0938462 1.5744671
> )
> 15 N tau( 15) = ( -0.1591043 0.0878842 1.5744671
> )
> 16 N tau( 16) = ( 0.0034422 -0.1817305 1.5744671
> )
> 17 N tau( 17) = ( 0.1556621 -0.0938462 0.1519033
> )
> 18 N tau( 18) = ( -0.1591043 -0.0878842 0.1519033
> )
> 19 N tau( 19) = ( 0.0034422 0.1817305 0.1519033
> )
> 20 N tau( 20) = ( -0.0139315 0.2264700 1.0041779
> )
> 21 N tau( 21) = ( -0.1891630 -0.1253001 1.0041779
> )
> 22 N tau( 22) = ( 0.2030945 -0.1011699 1.0041779
> )
> 23 N tau( 23) = ( -0.0139315 -0.2264700 0.7221925
> )
> 24 N tau( 24) = ( -0.1891630 0.1253001 0.7221925
> )
> 25 N tau( 25) = ( 0.2030945 0.1011699 0.7221925
> )
> 26 N tau( 26) = ( 0.3676808 -0.2000458 0.7412862
> )
> 27 N tau( 27) = ( -0.0105956 0.4184438 0.7412862
> )
> 28 N tau( 28) = ( -0.3570852 -0.2183980 0.7412862
> )
> 29 N tau( 29) = ( 0.3676808 0.2000458 0.9850842
> )
> 30 N tau( 30) = ( -0.0105956 -0.4184438 0.9850842
> )
> 31 N tau( 31) = ( -0.3570852 0.2183980 0.9850842
> )
> 32 N tau( 32) = ( 0.5127756 0.1138545 0.7287873
> )
> 33 N tau( 33) = ( -0.3549887 0.3871495 0.7287873
> )
> 34 N tau( 34) = ( -0.1577869 -0.5010040 0.7287873
> )
> 35 N tau( 35) = ( 0.5127756 -0.1138545 0.9975831
> )
> 36 N tau( 36) = ( -0.3549887 -0.3871495 0.9975831
> )
> 37 N tau( 37) = ( -0.1577869 0.5010040 0.9975831
> )
> 38 Sn tau( 38) = ( -0.0014732 -0.4102001 1.2238930
> )
> 39 Sn tau( 39) = ( 0.3559803 0.2038242 1.2238930
> )
> 40 Sn tau( 40) = ( -0.3545071 0.2063759 1.2238930
> )
> 41 Sn tau( 41) = ( -0.0014732 0.4102001 0.5024774
> )
> 42 Sn tau( 42) = ( 0.3559803 -0.2038242 0.5024774
> )
> 43 Sn tau( 43) = ( -0.3545071 -0.2063759 0.5024774
> )
> 44 Ge tau( 44) = ( -0.3506754 0.2104528 0.5754626
> )
> 45 Ge tau( 45) = ( -0.0069197 -0.4089202 0.5754626
> )
> 46 Ge tau( 46) = ( 0.3575951 0.1984674 0.5754626
> )
> 47 Ge tau( 47) = ( 0.3575880 0.1984633 0.5754510
> )
> 48 Ge tau( 48) = ( -0.0069197 -0.4089120 0.5754510
> )
> 49 Ge tau( 49) = ( -0.3506683 0.2104487 0.5754510
> )
> 50 Ge tau( 50) = ( -0.1808480 0.3132379 0.8631852
> )
> 51 Ge tau( 51) = ( 0.3616960 -0.0000000 0.8631852
> )
> 52 Ge tau( 52) = ( -0.1808480 -0.3132379 0.8631852
> )
> 53 Sn tau( 53) = ( 0.1771154 -0.3067729 0.8631852
> )
> 54 Sn tau( 54) = ( -0.3542309 -0.0000000 0.8631852
> )
> 55 Sn tau( 55) = ( 0.1771154 0.3067729 0.8631852
> )
> 56 N tau( 56) = ( 0.0000000 -0.0000000 0.4022443
> )
> 57 N tau( 57) = ( -0.0000000 -0.0000000 1.3241261
> )
> 58 Sn tau( 58) = ( -0.0000000 -0.0000000 0.6427795
> )
> 59 Sn tau( 59) = ( 0.0000000 -0.0000000 1.0835909
> )
>
> i.e. there are 3 Ge atoms more than expected (the count for the other
> atoms is OK). And one can see that atoms 44/49, 45/48 and 46/47 are at
> nearly the same positions. But of course with these positions added
> automatically by pw.x the calculation cannot progress. How can this have
> happened? There is something wrong here.
>
> Best regards,
>
> --
> José C. Conesa
> Research Professor
> Instituto de Catálisis y Petroleoquímica, CSIC
> Marie Curie, 2; Campus de Cantoblanco
> 28028 Madrid (Spain)
> Telef. +34 915854766
>
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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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