[Wien] w2web, StructGen
Dear Zhiyong Zhang, You should look at the user guide page 40: For R lattice use rhombohedral coordinates. (To convert from hexagonal into rhombohedral coordinates use the auxiliary program hex2rhomb, which can be called at a command-line: Regards Xavier Dear All, I am trying to use w2web to generate structures for Bi2Se3. I chose the space group R-3m and entered the three non-equivalent atoms. However, the generated structure seem to be incorrect as only one of the three equivalent positions of Atom 3 are generated. Even if I use and upload the the cif file I still got the same structure file. I have included the generated structures below. Thanks a lot, Zhiyong blebleble R LATTICE,NONEQUIV.ATOMS: 3166_R-3m MODE OF CALC=RELA unit=bohr 7.829135 7.829135 54.114198 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0.4008 MULT= 6 ISPLIT= 8 ATOM -1:X= 0. Y=0. Z=0.5992 ATOM -1:X= 0. Y=0.4008 Z=0. ATOM -1:X= 0. Y=0.5992 Z=0. ATOM -1:X= 0.4008 Y=0. Z=0. ATOM -1:X= 0.5992 Y=0. Z=0. Bi NPT= 781 R0=0.0500 RMT=1.5100 Z: 83.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.0001 Y=0. Z=0.2117 MULT= 6 ISPLIT= 8 ATOM -2:X= 0. Y=0. Z=0.7883 ATOM -2:X= 0. Y=0.2117 Z=0.0001 ATOM -2:X= 0. Y=0.7883 Z=0. ATOM -2:X= 0.2117 Y=0.0001 Z=0. ATOM -2:X= 0.7883 Y=0. Z=0. Se NPT= 781 R0=0.5000 RMT=0.8000 Z: 34.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -3: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 8 Se NPT= 781 R0=0.5000 RMT=0.8000 Z: 34.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0 NUMBER OF SYMMETRY OPERATIONS ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error
Dear Wien2k Users, I am calculating the ENE of a metastable phase. My approach is the following 1. Calculate ENE without spin orbit 2. Calculate ENE with spin orbit 2. Volume optimization of the structure For 1, I had to choose global energy parameter as 1.70 as the Fermi energy was surprisingly very high (approx 1.83). Though the SCF converged with some warning messages in the ENE value (in scf file), I had chosen Global energy parameter as 1.70 to remove the warning messages. In case of 2, keeping the energy parameter as 1.70, SCF gave errors in the 3rd cycle. The lapw2.error file showed the following 'FERMI' - EFERMI OUT OF ENERGY RANGE 'FERMI' - STOP IN EFI 'FERMI' - ENERGY OF LOWER BOUND : 0.22149 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.0 'FERMI' - ENERGY OF UPPER BOUND : 0.89041 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 4.0 'FERMI' - ADD4.0 'FERMI' - SOS 0.0060.0090......0040.0250.000 'FERMI' - NOS ** Any suggestions if I have to change the energy parameter to a smaller value. Suddhasattwa Ghosh -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100304/a66fdc56/attachment.htm
[Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error
If your fermi energy is really that high, you may have to increase EMAX in case.in1 (last line), otherwise you do not have enough eigenvalues to fill in all your electrons. Ghosh SUDDHASATTWA schrieb: Dear Wien2k Users, I am calculating the ENE of a metastable phase. My approach is the following 1. Calculate ENE without spin orbit 2. Calculate ENE with spin orbit 2. Volume optimization of the structure For 1, I had to choose global energy parameter as 1.70 as the Fermi energy was surprisingly very high (approx 1.83). Though the SCF converged with some warning messages in the ENE value (in scf file), I had chosen Global energy parameter as 1.70 to remove the warning messages. In case of 2, keeping the energy parameter as 1.70, SCF gave errors in the 3^rd cycle. The lapw2.error file showed the following ?FERMI' - EFERMI OUT OF ENERGY RANGE 'FERMI' - STOP IN EFI 'FERMI' - ENERGY OF LOWER BOUND : 0.22149 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.0 'FERMI' - ENERGY OF UPPER BOUND : 0.89041 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 4.0 'FERMI' - ADD 4.0 'FERMI' - SOS 0.0060.0090......0040.0250.000 'FERMI' - NOS ** Any suggestions if I have to change the energy parameter to a smaller value. Suddhasattwa Ghosh ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error
Dear Dr.Blaha, Thanks for the reply. The error which I had posted was with EMAX of 2.50. Suddhasattwa -Original Message- From: wien-boun...@zeus.theochem.tuwien.ac.at [mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Peter Blaha Sent: Thursday, March 04, 2010 12:09 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error If your fermi energy is really that high, you may have to increase EMAX in case.in1 (last line), otherwise you do not have enough eigenvalues to fill in all your electrons. Ghosh SUDDHASATTWA schrieb: Dear Wien2k Users, I am calculating the ENE of a metastable phase. My approach is the following 1. Calculate ENE without spin orbit 2. Calculate ENE with spin orbit 2. Volume optimization of the structure For 1, I had to choose global energy parameter as 1.70 as the Fermi energy was surprisingly very high (approx 1.83). Though the SCF converged with some warning messages in the ENE value (in scf file), I had chosen Global energy parameter as 1.70 to remove the warning messages. In case of 2, keeping the energy parameter as 1.70, SCF gave errors in the 3^rd cycle. The lapw2.error file showed the following 'FERMI' - EFERMI OUT OF ENERGY RANGE 'FERMI' - STOP IN EFI 'FERMI' - ENERGY OF LOWER BOUND : 0.22149 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.0 'FERMI' - ENERGY OF UPPER BOUND : 0.89041 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 4.0 'FERMI' - ADD 4.0 'FERMI' - SOS 0.0060.0090......0040.0250.000 'FERMI' - NOS ** Any suggestions if I have to change the energy parameter to a smaller value. Suddhasattwa Ghosh ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Birch-Murnaghan equation of state
Dear Wien2k Users, After volume optimization if we plot V vs E using different SCF files we get a plot showing fitting of Murnaghan equation of state. If we want to see the plotting for fitting of * Birch-Murnaghan* equation of state what should we do?we are getting V0 and E0 for both the fitting Murnaghan and Birch-Murnaghan equation of state but the plot showing fitting of only the Murnaghan equation of state. Thanks in advance. regards, Shamik Chakrabarti -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100304/71da5ec6/attachment.htm
[Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error
Dear Dr.Blaha, I had chosen the option in1 switch, the following error came 'FERMI' - EFERMI OUT OF ENERGY RANGE 'FERMI' - STOP IN EFI 'FERMI' - ENERGY OF LOWER BOUND : 0.22149 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.0 'FERMI' - ENERGY OF UPPER BOUND : 0.89041 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 4.0 'FERMI' - ADD4.0 'FERMI' - SOS 0.0060.0090......0040.0250.000 'FERMI' - NOS ** -Original Message- From: wien-boun...@zeus.theochem.tuwien.ac.at [mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Peter Blaha Sent: Thursday, March 04, 2010 12:09 PM To: A Mailing list for WIEN2k users Subject: Re: [Wien] [Wien2k Users] Error in 3rd SCF cycle: FERMI error If your fermi energy is really that high, you may have to increase EMAX in case.in1 (last line), otherwise you do not have enough eigenvalues to fill in all your electrons. Ghosh SUDDHASATTWA schrieb: Dear Wien2k Users, I am calculating the ENE of a metastable phase. My approach is the following 1. Calculate ENE without spin orbit 2. Calculate ENE with spin orbit 2. Volume optimization of the structure For 1, I had to choose global energy parameter as 1.70 as the Fermi energy was surprisingly very high (approx 1.83). Though the SCF converged with some warning messages in the ENE value (in scf file), I had chosen Global energy parameter as 1.70 to remove the warning messages. In case of 2, keeping the energy parameter as 1.70, SCF gave errors in the 3^rd cycle. The lapw2.error file showed the following 'FERMI' - EFERMI OUT OF ENERGY RANGE 'FERMI' - STOP IN EFI 'FERMI' - ENERGY OF LOWER BOUND : 0.22149 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.0 'FERMI' - ENERGY OF UPPER BOUND : 0.89041 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 4.0 'FERMI' - ADD 4.0 'FERMI' - SOS 0.0060.0090......0040.0250.000 'FERMI' - NOS ** Any suggestions if I have to change the energy parameter to a smaller value. Suddhasattwa Ghosh ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Birch-Murnaghan equation of state
Dear Peter Blaha Sir, Thank you very much for your reply. My problem is resolved. regards, Shamik Chakrabarti On Thu, Mar 4, 2010 at 1:20 PM, Peter Blaha pblaha at theochem.tuwien.ac.atwrote: Useeplot_lapw from the commandline. or plot case.eosfitb with your favorite plotting program. shamik chakrabarti schrieb: Dear Wien2k Users, After volume optimization if we plot V vs E using different SCF files we get a plot showing fitting of Murnaghan equation of state. If we want to see the plotting for fitting of *Birch-Murnaghan* equation of state what should we do?we are getting V0 and E0 for both the fitting Murnaghan and Birch-Murnaghan equation of state but the plot showing fitting of only the Murnaghan equation of state. Thanks in advance. regards, Shamik Chakrabarti ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100304/7d40e563/attachment.htm
[Wien] Bad formation energies for the charged vacancies
Hi Laurence,
Sorry for the delay in getting back
I think the issue is that at present Wien2k does not really add a
constant charge background and calculate the self-energy of this
charge (in a given potential), it instead add the potential associated
with this charge.
Yes, sounds like that may be the issue. Because the neutralizing
background charge is not actually being added to the remaining
physical charge, and carried along with the physical charge at all
points, the total energy is not uniquely defined.
If one has N-1 electrons, a nuclear charge of N,
only N-1 eigenvalues are calculated, no eigenvalue for a flat
background (of course one would not get a flat eigenvalue).
Right. Ideally, the N-1 states would be used to construct the physical
part of the density, then the constant neutralizing background would
be added to that to construct the total. If this is not the case, then
there will be inconsistencies/ambiguities.
You can see this by doing a calculation of an H+ ion in a cell with no
electrons. The results one will get is -ve, i.e. it is the energy of a
H+ ion in the background potential. This is not the same as the energy
of an H+ ion in vacuum.
(... which we should approach in the limit of infinite cell dimension.)
The question is then how to do a realistic charged cell calculation
with meaningful energies taking account of the effect of a potential
shift? If vacuum is available one can determine the potential shift
and correct; one can also calibrate the value of a core level and use
this to determine the shift (with reservations) but it would be nice
to have a more elegant method..
One answer (e.g., Makov-Payne and others) is to always neutralize non-
neutral cells with a constant background so that there are no
arbitrary constants in energies. Then correct the resulting energies
with multipole terms which vanish as L^-1, L^-3, etc. (L = cell dim.)
to aid convergence to the (unique) infinite-L limit.
However, some recent work, in the context of defects in condensed
matter, seeks to compute and apply potential shifts to define
meaningful energies: e.g.,
Title: Accurate prediction of defect properties in density functional
supercell calculations
Author(s): Lany S, Zunger A
Source: MODELLING AND SIMULATION IN MATERIALS SCIENCE AND
ENGINEERING Volume: 17 Issue: 8Article Number: 084002 Published:
DEC 2009
Note, though, that here too there is some arbitrariness, e.g., in
defining the site potentials. In any case, possibly some of the
ideas could be of help?
John
On Fri, Feb 26, 2010 at 5:30 PM, John Pask pask1 at llnl.gov wrote:
Hi Peter,
In the integrals below, \rho is just the electronic charge density
(without nuclei).
Thus c \int{\rho] does NOT vanish and gives c * NE (number of
electrons).
However, if rho comes from electronic states, each eigenvalue is
shifted
by the constant c
and thus the sum of eigenvalues cancels the c * NE term
However, when I add a background charge to neutralize the unit
cell,
this does not come
from any eigenvalue, so if I handle this in the usual way, \rho
will now
integrate to
NE + Q, and I get an extra c * Q term, which is not compensated by
an
eigenvalue.
Actually, in the integrals below, \rho is the *total* (electronic +
nuclear)
charge, which must be net neutral to have a well-defined total energy
(otherwise energy diverges).
With regard to the present question on charged-cell calculations,
the point
is just that the calculation must be performed on a neutralized
cell in
order to have well-defined total energy. So the Kohn-Sham
calculation is
performed on a neutral cell, whether or not the physical system is
charged,
and the corrections for non-neutrality, if any (e.g., Makov-Payne,
Eq.
(15)), are added after.
So as long as the neutralizing charge enters all potential and energy
expressions along with the physical charge, so that all expressions
operate on a net-neutral total, the Kohn-Sham total energy must be
invariant
to arbitrary constants in V (because the total Coulomb energy is).
John
John Pask schrieb:
Dear Peter,
Yes, the background charge must be taken into account as part of
the
net-neutral total charge in order to have well-defined total
energy. Then as
long as the compensation charge is then in exactly the same way
as the
remaining physical charge (i.e., enters all the same
integrals), then the
arbitrary constant in potential should not matter since:
\int{ \rho (V + c)} = \int{ \rho V} + c \int{ \rho} = \int
{\rho V},
independent of arbitrary constant c.
John
On Feb 24, 2010, at 11:54 PM, Peter Blaha wrote:
Is the question regarding the computation of total energy per
unit
cell in an infinite crystal with non-neutral unit cells? If
so, then the
total energy diverges -- and so is not well-defined. (So
neutralizing
backgrounds must be added in such cases
