Right!!! Sorry!!
On Wed, Apr 9, 2008 at 1:58 PM, Eduardo Anglada <[EMAIL PROTECTED]> wrote:
>
> >
> > Excuse-me, but have u noticed that you cut off for all basis is ZERO?!
> > It means that all of your electrons are confined to the nucleous...
> >
>
> Sorry but, No. It means: use siesta heuristics (energy shift and split
> norm) in order to determine the rc.
>
> Regards,
> Eduardo
>
>
>
>
> >
> >
>
>
> > all of then, n this way u have no bonds formation and a huge
> > electronic repulsion I would say ... U need to especiffy your cut off
> > radius resoanably!
> >
> > Cheers..
> >
> > NH
> > On Wed, Apr 9, 2008 at 1:13 PM, Nidhi Sharma <[EMAIL PROTECTED]>
> wrote:
> >
> > > Hi,
> > >
> > > I have made the changes according to u and defined the pseudo of Sm as
> > > pg Samarium
> > > tm2 3.0 # PS flavor, logder R
> > > n=Sm c=ca # Symbol, XC flavor,{ |r|s}
> > >
> > > 0.0 0.0 0.0 0.0 0.0 0.0
> > > 11 4 # norbs_core, norbs_valence
> > > 6 0 2.00 0.00 # 6s2
> > > 6 1 0.00 0.00 # 6p0
> > > 5 2 0.00 0.00 # 5d0
> > > 4 3 6.00 0.00 # 4f6
> > > 3.11 4.10 3.11 3.11 0.00 0.00
> > > and Te as
> > > pg Tellurum
> > > tm2 3.0
> > > n=Te c=ca
> > > 0.0 0.0 0.0 0.0 0.0 0.0
> > > 9 3
> > >
> > > 5 0 2.00 0.00
> > > 5 1 4.00 0.00
> > > 5 2 0.00 0.00
> > > 2.57 2.63 2.57
> > > but when I define the PAO basis like
> > >
> > > %block PAO.Basis
> > > Sm 2 # Label, l-shells
> > > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=6 1 2
> > >
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=5 2 2
> > >
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=4 3 2
> > >
> > > 0.000 0.000
> > > 1.000 1.000
> > > Te 2 # Species label, number of l-shells
> > > n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=5 1 2 # n, l, Nzeta
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=5 2 2 # n, l, Nzeta
> > > 0.000 0.000
> > > 1.000 1.000
> > > %endblock PAO.Basis
> > >
> > >
> > > Then I got this kind of error on the command line
> > >
> > > reinit:
> > > -----------------------------------------------------------------------
> > > reinit: System Name: SmTe
> > > reinit:
> > > -----------------------------------------------------------------------
> > > reinit: System Label: SmTe
> > > reinit:
> > > -----------------------------------------------------------------------
> > >
> > >
> > >
> > > initatom: Reading input for the pseudopotentials and atomic orbitals
> > > ----------
> > > Species number: 1 Label: Sm Atomic number: 62
> > > Species number: 2 Label: Te Atomic number: 52
> > > Ground state valence configuration: 6s02 4f06
> > > Reading pseudopotential information in formatted form from Sm.psf
> > > Ground state valence configuration: 5s02 5p04
> > > Reading pseudopotential information in formatted form from Te.psf
> > > WRONG species symbol in PAO.Basis: n
> > >
> > > Stopping Program from Node: 0
> > > Again I mabe the changes in PAO basis as
> > > %block PAO.Basis
> > > Sm 2 # Label, l-shells
> > > n=6 0 2 P 1 # n, l, Nzeta, Polarization,
> NzetaPol
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=4 3 2
> > >
> > > 0.000 0.000
> > > 1.000 1.000
> > > Te 2 # Species label, number of l-shells
> > > n=5 0 2 P 1 # n, l, Nzeta, Polarization,
> NzetaPol
> > > 0.000 0.000
> > > 1.000 1.000
> > > n=5 1 2 # n, l, Nzeta
> > > 0.000 0.000
> > > 1.000 1.000
> > > %endblock PAO.Basis
> > >
> > > then the program run successfully but lattice parameter and band gap is
> far
> > > from our expt values. May you please check my .fdf file and guide me
> where
> > > should make the appropriate changes. I m enclosing .fdf file, .out
> file,
> > > psf file and band structure (looks like metallic) that we obtained.
> > >
> > > Many thanks in advance.
> > >
> > >
> > > [EMAIL PROTECTED] wrote:
> > >
> > > You mix up several things; I doubt it will help to resolve your problems
> > > but let us address them one by one.
> > >
> > > Sm valence configuration. 4f states are quite localized and
> > > probably (in reality, not in DFT the calculation) are not any near
> > > to the band gap. If you include them in valence states and in the basis,
> > > your trouble will be not performing the calculation as such,
> > > but their wrong calculated positioning (at the Fermi level).
> > > If you attribute them to core... I don't know there is an easy way
> > > to do this, because the 4f shell is not fully occupied.
> > > Search for previous calculations (any method, with DFT and beyond)
> > > on RE chalcogenides, and on any RE calculations using pseudopotentials.
> > >
> > >
> > > > Dear users, as we know the valence configuration of Sm is 4f6,6s2. In
> > > > order to combine it with chalcogenides it is necessary to make the net
> > > > ionic charge of Sm to 2, means we have to consider the 4f6 in the
> core.
> > > >
> > >
> > > Why necessary? The "net ionic charge", whatever its definition, will
> come
> > > out of your calculation somehow. To begin with, you start from neutral
> > > atoms, and they remain neutral, whether you attribute 4f to the core
> > > or to the valence states...
> > >
> > >
> > > > When we define the PAO basis set as
> > > >
> > > > %block PAO.Basis
> > > > Sm 2 # Label, l-shells
> > > > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> > > > 0.000 0.000
> > > > 1.000 1.000
> > > >
> > >
> > > Don't forget to include 5d in the basis; they are IMPORTANT.
> > >
> > >
> > > > Te 2 # Species label, number of l-shells
> > > > n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> > > > 0.000 0.000
> > > > 1.000 1.000
> > > > n=5 1 2 # n, l, Nzeta
> > > > 0.000 0.000
> > > > 1.000 1.000
> > > > %endblock PAO.Basis
> > > >
> > >
> > > Your Te might be OK (or not); at least no obvious faults.
> > >
> > >
> > > >
> > > > it will display the following message
> > > > reinit:
> > > > reinit: System Label: SmTe
> > > >
> -----------------------------------------------------------------------
> > > > initatom: Reading input for the pseudopotentials and atomic orbitals
> > > > ----------
> > > > Species number: 1 Label: Sm Atomic number: 62
> > > > Species number: 2 Label: Te Atomic number: 52
> > > > Ground state valence configuration: 6s02 4f06
> > > > Reading pseudopotential information in formatted form from Sm.psf
> > > > Ground state valence configuration: 5s02 5p04
> > > > Reading pseudopotential information in formatted form from Te.psf
> > > > Bad format of (n), l, nzeta line in PAO.Basis
> > > > Stopping Program from Node: 0
> > > >
> > >
> > > This is probably because you promised 2 functions in the basis block for
> Sm
> > > but passed only one (6s). Make it consistent.
> > >
> > >
> > > > If I include the 4f6 in basis set it will make the net charge 8 and
> behave
> > > > as a semi core.
> > > >
> > >
> > > This "net charge" is not exactly your worry. It simply gives you the
> number
> > > of electrons provided by the atom in question to the valence band,
> > > in does not yet make from Sm a 8+ ion. Similarly, you can choose
> > > the Te configuration either as 5s2 5p4 5d0 (6 valence electrons)
> > > or 5s2 5p4 4d10 (16 valence electrons), it is still the same atom.
> > > Only, you'll have different number of bands. I repeate, the decision
> > > to put Sm 4f in the core or in the valence is only your - difficult,
> > > but free - choice.
> > >
> > > Now we come to Te.
> > >
> > >
> > > > If I use a already generated pseudo file of Te which include 5s2, 5p4,
> 4d0
> > > > and 4f0 But how can 4d0 is possible although it contains 10 electrons.
> > > >
> > >
> > > This is a misprint in the head line of the Te pseudo. It was generated
> > > with 4d10 in the core and 5d as valence states. (Ask Eduardo Anglada).
> > >
> > >
> > > > When I use this file then we get results but band gap in B1 phase
> > > > is ~10eV which is quite far from the expt 0.67eV.
> > > >
> > >
> > > This can be due to anything. (In fact an absence of Sm5d in the basis
> > > is a good candidate). Try to look not only at the band gap value
> > > (which will be wrong anyway) but at the density of states,
> > > positioning of different groups of valence bands. The band structure
> > > of RE chalcogenides is well known.
> > >
> > >
> > > > Please help me how can i resolve the problem of valence charge .
> > > >
> > >
> > > I don't see there is a problem, in fact. The (technical) problem is -
> > > if you want to remove 4f from the valence - how to declare them as core,
> > > even as this shell is not fully occupied. But by default, you can
> > > go ahead with 4f as valence states (in BOTH basis and pseudopotential).
> > > Then you'll see that the positioning of the 4f is wrong, and start
> > > to think how bad this is for the problem your have to solve,
> > > and what to do about it. This is not a SIESTA problem, but one
> > > which appeared before in other DFT calculations.
> > >
> > > Good luck,
> > >
> > > Andrei Postnikov
> > >
> > >
> > >
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