[Pw_forum] Conserving the same Wyckoff multiplicity in the input and in the output
hqtst42
hqtst42 at netc.pl
Thu Apr 20 04:35:39 CEST 2017
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
>
> _______________________________________________
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-------------- next part --------------
&control
calculation = 'relax',
restart_mode = 'from_scratch',
prefix = 'testmol',
verbosity = 'default' ,
tstress = .true.,
tprnfor = .true.,
pseudo_dir = '../',
outdir = '/tmp/exec-for-all/',
etot_conv_thr = 0.0001 ,
nstep = 100,
/
&system
ibrav = -12
space_group = 14
use_all_frac = .true.
A = 14.667,
B = 7.886,
C = 10.730,
cosAB = 0,
cosAC = -0.084947397,
cosBC = 0,
nat = 33
ntyp = 3
ecutwfc =50.0
spline_ps = .true.
tot_charge = 0
/
&electrons
electron_maxstep = 100,
conv_thr = 1.0D-6 ,
startingpot = 'atomic' ,
startingwfc = 'atomic' ,
mixing_mode = 'plain' ,
mixing_beta = 0.7D0 ,
mixing_ndim = 8,
diagonalization = 'david' ,
scf_must_converge = .FALSE. ,
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
C 12.010 C.pbe-tm-new-gipaw-dc.UPF
H 1.007 H.pbe-tm-new-gipaw-dc.UPF
O 15.999 O.pbe-tm-new-gipaw-dc.UPF
ATOMIC_POSITIONS (crystal_sg)
C 0.41617 0.3483 0.3962
C 0.35013 0.2207 0.3217
C 0.3996 0.1089 0.2383
C 0.30378 0.1238 0.4203
C 0.21726 0.1726 0.4466
C 0.17604 0.0902 0.5385
C 0.22027 -0.0484 0.6065
C 0.30785 -0.0965 0.5821
C 0.34864 -0.0127 0.4879
C 0.17414 -0.1385 0.7045
C 0.09696 -0.2639 0.6467
C 0.0414 -0.3210 0.7486
C 0.1373 -0.4152 0.5836
O 0.37920 0.4968 0.4148
O 0.49690 0.3117 0.4375
H 0.4247 0.5665 0.4693
H 0.2948 0.2919 0.2600
H 0.4571 0.0403 0.2956
H 0.4299 0.1810 0.1712
H 0.3514 0.0176 0.1875
H 0.1812 0.2830 0.3945
H 0.1097 0.1262 0.5560
H 0.3458 -0.1972 0.6359
H 0.4175 -0.0544 0.4738
H 0.2270 -0.2108 0.7714
H 0.1455 -0.0431 0.7647
H 0.0510 -0.1936 0.5721
H 0.0865 -0.3837 0.8247
H 0.0101 -0.2159 0.7895
H -0.0163 -0.4031 0.7025
H 0.1799 -0.3750 0.5153
H 0.0799 -0.4965 0.5345
H 0.1806 -0.4871 0.6535
K_POINTS automatic
1 1 1 1 1 1
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