[Thermo_pw-forum] nonstoichiometric compounds
Andrea Dal Corso
dalcorso at sissa.it
Sat Oct 8 16:02:14 CEST 2016
This is not a problem of thermo_pw. If you use the same input with
pw.x you will have only four symmetry operations as well. The problem
is that using ibrav=6 with 24 atoms the
code finds that it is a supercell and neglects all symmetries with
fractional translations.
Although slow however this cell is correct and should provide
reasonable results.
thermo_pw just tells you that you are not exploiting correctly the symmetry.
If you use ibrav=7 without converting the coordinates to the centered
cell, the coordinates are
wrong because they are in the crystal basis of the conventional cell
and the atoms should be 12.
cif2qe should now have an option that allow you to obtain the crystal
coordinates for the centered cell.
The alternative is to use the QE ability to deal directly with the
space group.
You have to specify space_group=141 and origin_choice=2 in the system
namelist, to use
nat=2 because there are only two inequivalent atoms and specify the
atomic coordinates as crystal_sg,
giving
V 16h 0.49964 0.26712
H 8c
extracted from your cif file. With this input QE finds a cell with ibrav=7,
and 12 atoms and thermo_pw recognizes correctly the space group 141
and finds a point group D_4h
compatible with the centered tetragonal lattice.
HTH,
Andrea
Quoting Gunnar Palsson <gunnar.karl at gmail.com>:
> Dear Andrea,
>
>
> I have obtained a cif file for the stoichiometric compound V2H and I
> have run cif2cell (1.2.10) to generate a pw input file. Since the
> cell is body centered tetragonal I changed the Bravais lattice to 7.
> When running thermo_pw to calculate the phonon dispersion, the
> program mentions that there is an incompatibility of the point group
> with the Bravais lattice.
>
> However if I run the cif2cell with the following option: cif2cell
> v2h.cif -p pwscf --no-reduce --print-symmetry-operations I get 32
> symmetry operations.
>
> The output of thermo_pw (0.5.0) running on QE 5.4.0 is:
>
> C_i (-1) is incompatible with the centered tetragonal Bravais lattice
> It is compatible with the
> triclinic Bravais lattice; ibrav= 14
>
> You might want to change the Bravais lattice or to
>
> understand why the symmetries are wrong beforecontinuing
> The point group or the Laue class are not used to reduce the number of
> computed tensor components
> Found symmetry operation: I + ( 0.5000 -0.5000 -0.5000)
> This is a supercell, fractional translations are disabled
>
> FFT mesh: ( 50, 50, 50 )
>
> 2 Sym. Ops., with inversion, found
>
>
> 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 inversion
>
> cryst. s( 2) = ( -1 0 0 )
> ( 0 -1 0 )
> ( 0 0 -1 )
>
>
> cart. s( 2) = ( -1.0000000 0.0000000 0.0000000 )
> ( 0.0000000 -1.0000000 0.0000000 )
> ( 0.0000000 0.0000000 -1.0000000 )
>
>
> point group C_i (-1)
> there are 2 classes
> the character table:
>
> E i
> A_g 1.00 1.00
> A_u 1.00 -1.00
>
>
> Changing the Bravais lattice to 6 yields a different response:
>
> C_2h (2/m) is incompatible with the tetragonal Bravais lattice
> It is compatible with the
> monoclinic (c unique) Bravais lattice; ibrav= 12
> base centered monoclinic (c unique) Bravais lattice; ibrav= 13
> monoclinic (b unique) Bravais lattice; ibrav= -12
> base centered monoclinic (b unique) Bravais lattice; ibrav= -13
>
> You might want to change the Bravais lattice or to
>
> understand why the symmetries are wrong beforecontinuing
> The point group or the Laue class are not used to reduce the number of
> computed tensor components
> Found symmetry operation: I + ( -0.5000 -0.5000 -0.5000)
> This is a supercell, fractional translations are disabled
>
> FFT mesh: ( 60, 60, 64 )
>
> 4 Sym. Ops., with inversion, found
>
>
> 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 [1,0,0]
>
> cryst. s( 2) = ( 1 0 0 )
> ( 0 -1 0 )
> ( 0 0 -1 )
>
> cart. s( 2) = ( 1.0000000 0.0000000 0.0000000 )
>
> 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 [1,0,0]
>
> cryst. s( 4) = ( -1 0 0 )
> ( 0 1 0 )
> ( 0 0 1 )
>
> cart. s( 4) = ( -1.0000000 0.0000000 0.0000000 )
> ( 0.0000000 1.0000000 0.0000000 )
> ( 0.0000000 0.0000000 1.0000000 )
>
>
> point group C_2h (2/m)
> there are 4 classes
> the character table:
>
> I have spent a lot of time trying to figure this out but I am
> unable. Any advice would be most welcome,
>
> Best regards,
> Gunnar
>
>
>> On 16 Aug 2016, at 12:05, Andrea Dal Corso <dalcorso at sissa.it> wrote:
>>
>> On Sat, 2016-08-13 at 13:16 +0200, Gunnar Palsson wrote:
>>> Dear Andrea,
>>>
>>> First I would like to tell you that I find your thermo_pw package
>>> extremely useful in many ways. I was inspired by your article J.
>>> Phys. Condensed Matter 26, 335401 (2014) and have been practising
>>> using your PS library v1.0 and the PAW potentials, for pure
>>> vanadium and niobium to calculate the thermoelastic properties. I
>>> have been thinking for quite a while about calculating the
>>> thermophysical properties and changes in free energy of metal
>>> hydrides, specifically vanadium hydride, in an attempt to
>>> determine the phase boundaries. I am also interested in the
>>> changes in the elastic constants with temperature and hydrogen.
>>> The question I have is whether one can use thermo_pw to calculate
>>> the Helmholtz free energy in the quasi harmonic approximation as a
>>> function of temperature for a supercell of vanadium with few
>>> hydrogen atoms. The size of the supercell determines what part of
>>> the phase diagram one can access in terms of concentration. So for
>>> 16 vanadium atoms, one can go from
>> 1/
>>> 16 to 16/16 in H/V concentration for example. It is my
>>> understanding that this requires ibrav=0, which may not be fully
>>> implemented? If not it would still be valuable to look into the
>>> stoichiometric hydride, V2H, and VH. The V2H belongs to space
>>> group 141. Finally, I have some neutron scattering data on
>>> hydrogen containing vanadium, and it would be extremely valuable
>>> to use the output of thermo_pw to calculate various neutron
>>> scattering cross sections and compare with experiment, which I can
>>> probably do.
>>>
>> Using ibrav=0 thermo_pw cannot use symmetry to reduce the number of
>> tensor components that it calculates. Moreover it does not know the
>> Bravais lattice number and presently it cannot calculate it, so it
>> cannot find the automatic path, you have to provide it from input.
>> I think it might also be possible to use ibrav=0 for phonon calculations
>> and for the calculation of harmonic thermal properties, but all the
>> rest, such as the anharmonic properties is most probably uncorrect. In
>> any case I have not worked on this option so far, so I think it is very
>> probable that there are problems.
>>
>> Andrea
>>
>>> Best regards,
>>> Dr. Gunnar Palsson,
>>> Researcher,
>>> Uppsala University.
>>> _______________________________________________
>>> Thermo_pw-forum mailing list
>>> Thermo_pw-forum at qeforge.qe-forge.org
>>> http://qeforge.qe-forge.org/mailman/listinfo/thermo_pw-forum
>>
>> --
>> Andrea Dal Corso Tel. 0039-040-3787428
>> SISSA, Via Bonomea 265 Fax. 0039-040-3787249
>> I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
>>
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