Re: [SIESTA-L] Valence configuration of samarium
Hi, I have made the changes according to u and defined the pseudo of Sm as Hi - If u refers to me, mind that I never advised you on the pseudo radii for Sm... I only meant that inclusing 4f is technically no error - but it will probably lead to physically wrong results. Whatever... Regarding your problems with calculations which sometimes stop at an error in basis block, sometimes not: you should carefully read the SIESTA doc file about the syntaxis of the basis block. Namely: 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 - yes, it fails, because you declared 2 l-shells (1st line of the Sm block) but in the following you pass the info for 4 l-shells. I thought we were already past this problem... 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. Now this is formally correct (number of l-shells declared equals number of l-shells passed), but the basis (at least for Sm) is not complete enough - you'd need 5d in the basis. And after you do this, do not expect to get band structure right, because 4f states will most probably be at a wrong energy... Good luck Andrei Postnikov
Re: [SIESTA-L] Valence configuration of samarium
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
114 # norbs_core, norbs_valence
60 2.00 0.00 # 6s2
61 0.00 0.00 # 6p0
52 0.00 0.00 # 5d0
43 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
93
50 2.00 0.00
51 4.00 0.00
52 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
Re: [SIESTA-L] Valence configuration of samarium
Nidhi, If you need 4f in the valence as semicore, then your line should have something like n=4 3 2 4f, double-zeta. Of course the number of zetas can vary, as well as the number of polarization functions. What is the electronic configuration of your Sm pseudo? Marcos Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Nidhi Sharma Hi to all, 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. 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 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 it will display the following message 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 Bad format of (n), l, nzeta line in PAO.Basis Stopping Program from Node:0 If I include the 4f6 in basis set it will make the net charge 8 and behave as a semi core. 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. 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. Please help me how can i resolve the problem of valence charge . Thanks in advance. Nidhi - Did you know? You can CHAT without downloading messenger. Click here -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain 1 Place Croix du Sud, B-1348 Louvain-la-Neuve Belgique -- Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto.
Re: [SIESTA-L] Valence configuration of samarium
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
