Re: [Pw_forum] Incomplete output in HSE calculation

[Paolo Giannozzi]

The code first performs a self-consistent calculation without the exact
exchange potential. Next iterations are MUCH slower than the first one. If
the code is still running, just wait; if not, it might have crashed due to
insufficient memory or other reasons

Paolo

On Wed, Nov 18, 2015 at 7:18 AM, Vipul Shivaji Ghemud <
vi...@physics.unipune.ac.in> wrote:

> I am doing HSE calculation, and using following flags. But, the output
> reads:
>
> the Fermi energy is 7.8327 ev
> convergence has been achieved in  33 iterations
>
> But, it is not writing Total energy and other outputs. The input is as
> follows:
>
> input_dft='HSE'
> exx_fraction=0.25,
> screening_parameter=0.2,
> exxdiv_treatment='vcut_spherical',
> x_gamma_extrapolation=.false
>
> Is there anything else i need to add?
> --
> Vipul S. Ghemud
> Ph.D. student.
> Dept of Physics,
> SPPU, Ganeshkhind,
> Pune- 411007.
>
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-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] ZHEGV ERROR

[Jure Varlec]

In addition to what Giovanni wrote, I do not recommend using VESTA for
generating data for further processing. It is meant to produce pretty
pictures (which it does rather well), and that means it tends to
include atoms from neighbouring images to make the unit cell look
"complete". This causes overlaps.

Regards
Jure

On Tue, 17 Nov 2015 21:07:26 +
tomy tunde  wrote:

> Dear All,
>  I tried to build a supercell with VESTA for MgB2 and I was have this
> error.
> %%
> task #        0 from cdiaghg : error #      129
>     diagonalization (ZHEGV*) failed
>  
> Although, I tried to fixed the problem based on past post on this
> medium but it seems to be a difficult task.
> 
> Initial, I did some electronic structure calculations base on three
> atomic positions which are in agreement with previous works on it.
> However, the problem started when I tried to build a supercell of 30
> atoms with VESTA in order for me to dope it with other element, I was
> having this error message posted above. I will appreciate if anyone
> can tell me what is wrong with my input file or how I can go about
> solving this particular task. I appreciate all your kind gesture as I
> await your response. The input file is given below:
> 
> &control
>       calculation = 'scf'
>       restart_mode='from_scratch'
>       prefix='MgB2',
> pseudo_dir = '/home/work/espresso-5.0/pseudo/',
>     outdir='./'
> /
> &system
>     ibrav=4,
>     celldm(1)=11.66,
>     celldm(3)=1.14,
>     nat=30,
>       ntyp=2,
>     ecutwfc =35.0,
>       ecutrho =350.0,
>       occupations= 'smearing',
>     degauss= 0.03,
>       smearing= 'cold',
>  /
>   &electrons
>       mixing_beta = 0.7
>     conv_thr =  1.0d-12
>     diagonalization = 'cg'
> /
>  ATOMIC_SPECIES
>   Mg 24.3 Mg.pbe-n-rrkjus.UPF
>   B  10.8 B.pbe-n-rrkjus.UPF
> ATOMIC_POSITIONS  {angstrom}
> Mg          0.00  0.00  0.00
> Mg          -0.00  -0.00  1.00
> Mg          -0.00  1.00  0.00
> Mg          -0.00  1.00  1.00
> Mg          1.00  0.00  0.00
> Mg          1.00  -0.00  1.00
> Mg          1.00  1.00  0.00
> Mg          1.00  1.00  1.00
> B          -0.00  0.577350  0.571000
> B            1.00  0.577350  0.571000
> B            0.422650  0.422650  0.571000
> B            0.577350  0.00  0.571000
> B            0.577350  1.00  0.571000
> B          -0.00  0.422650  0.571000
> B            1.00  0.422650  0.571000
> B            0.577350  0.577350  0.571000
> B            0.422650  0.00  0.571000
> B            0.422650  1.00  0.571000
> B            0.50  0.288680  0.571000
> B            0.711320  0.211320  0.571000
> B            0.788680  0.50  0.571000
> B            0.50  0.711320  0.571000
> B            0.288680  0.788680  0.571000
> B            0.211320  0.50  0.571000
> B            0.711320  0.50  0.571000
> B            0.788680  0.288680  0.571000
> B            0.50  0.211320  0.571000
> B            0.288680  0.50  0.571000
> B            0.211320  0.711320  0.571000
> B            0.50  0.788680  0.571000
> K_POINTS {automatic}
> 18 18 9 0 0 0
> 
> 
> With best regards,Adeniji Rasaki idowurskaden...@yahoo.com
> 
>  
>  Reply, Reply All or Forward  |  More


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[Pw_forum] Incomplete output in HSE calculation

[Vipul Shivaji Ghemud]

I am doing HSE calculation, and using following flags. But, the output reads:

the Fermi energy is 7.8327 ev
convergence has been achieved in  33 iterations

But, it is not writing Total energy and other outputs. The input is as
follows:

input_dft='HSE'
exx_fraction=0.25,
screening_parameter=0.2,
exxdiv_treatment='vcut_spherical',
x_gamma_extrapolation=.false

Is there anything else i need to add?
-- 
Vipul S. Ghemud
Ph.D. student.
Dept of Physics,
SPPU, Ganeshkhind,
Pune- 411007.

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Re: [Pw_forum] ZHEGV ERROR

[Giovanni Cantele]

There is an evident problem with your input: the ATOMIC_POSITIONS card is 
wrong, because it corresponds to Mg-Mg distance of ~ 1 A and Mg-B distance of ~ 
0.7 A that do not look reasonable to me. So either the positions are all wrong 
or the units are wrong. Maybe you intended crystal units? In the case the 
present positions should be revised as well, because in crystal units atoms 
such as 
Mg  0.00  0.00  0.00
Mg  -0.00  -0.00  1.00
are equivalent.

I suggest to use visualization software, XCrysDen is usually quite helpful, 
being able to open directly Quantum-Espresso input/output files.

Giovanni

> On 17 Nov 2015, at 22:07, tomy tunde  wrote:
> 
> Dear All,
> I tried to build a supercell with VESTA for MgB2 and I was have this error.
> %%
> task #0
> from cdiaghg : error #  129
> diagonalization (ZHEGV*) failed
> 
> Although, I tried to fixed the problem based on past post on this medium
> but it seems to be a difficult task.
> 
> Initial, I did some electronic structure calculations base on three atomic
> positions which are in agreement with previous works on it. However, the
> problem started when I tried to build a supercell of 30 atoms with VESTA
> in order for me to dope it with other element, I was having this error
> message posted above. I will appreciate if anyone can tell me what is
> wrong with my input file or how I can go about solving this particular
> task. I appreciate all your kind gesture as I await your response. The
> input file is given below:
> 
> &control
>   calculation = 'scf'
>   restart_mode='from_scratch'
>   prefix='MgB2',
> pseudo_dir = '/home/work/espresso-5.0/pseudo/',
> outdir='./'
> /
> &system
> ibrav=4,
> celldm(1)=11.66,
> celldm(3)=1.14,
> nat=30,
>   ntyp=2,
> ecutwfc =35.0,
>   ecutrho =350.0,
>   occupations= 'smearing',
> degauss= 0.03,
>   smearing= 'cold',
> /
>   &electrons
>   mixing_beta = 0.7
> conv_thr =  1.0d-12
> diagonalization = 'cg'
> /
> ATOMIC_SPECIES
>   Mg 24.3 Mg.pbe-n-rrkjus.UPF
>   B  10.8 B.pbe-n-rrkjus.UPF
> ATOMIC_POSITIONS  {angstrom}
> Mg  0.00  0.00  0.00
> Mg  -0.00  -0.00  1.00
> Mg  -0.00  1.00  0.00
> Mg  -0.00  1.00  1.00
> Mg  1.00  0.00  0.00
> Mg  1.00  -0.00  1.00
> Mg  1.00  1.00  0.00
> Mg  1.00  1.00  1.00
> B  -0.00  0.577350  0.571000
> B1.00  0.577350  0.571000
> B0.422650  0.422650  0.571000
> B0.577350  0.00  0.571000
> B0.577350  1.00  0.571000
> B  -0.00  0.422650  0.571000
> B1.00  0.422650  0.571000
> B0.577350  0.577350  0.571000
> B0.422650  0.00  0.571000
> B0.422650  1.00  0.571000
> B0.50  0.288680  0.571000
> B0.711320  0.211320  0.571000
> B0.788680  0.50  0.571000
> B0.50  0.711320  0.571000
> B0.288680  0.788680  0.571000
> B0.211320  0.50  0.571000
> B0.711320  0.50  0.571000
> B0.788680  0.288680  0.571000
> B0.50  0.211320  0.571000
> B0.288680  0.50  0.571000
> B0.211320  0.711320  0.571000
> B0.50  0.788680  0.571000
> K_POINTS {automatic}
> 18 18 9 0 0 0
> 
> 
> With best regards,
> Adeniji Rasaki Idowu
> rskaden...@yahoo.com
> 
> 
> Reply, Reply All or Forward | More
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[Pw_forum] ZHEGV ERROR

[tomy tunde]

Dear All,
 I tried to build a supercell with VESTA for MgB2 and I was have this error.
%%
    task #        0
    from cdiaghg : error #      129
    diagonalization (ZHEGV*) failed
 
Although, I tried to fixed the problem based on past post on this medium
but it seems to be a difficult task.

Initial, I did some electronic structure calculations base on three atomic
positions which are in agreement with previous works on it. However, the
problem started when I tried to build a supercell of 30 atoms with VESTA
in order for me to dope it with other element, I was having this error
message posted above. I will appreciate if anyone can tell me what is
wrong with my input file or how I can go about solving this particular
task. I appreciate all your kind gesture as I await your response. The
input file is given below:

&control
      calculation = 'scf'
      restart_mode='from_scratch'
      prefix='MgB2',
pseudo_dir = '/home/work/espresso-5.0/pseudo/',
    outdir='./'
/
&system
    ibrav=4,
    celldm(1)=11.66,
    celldm(3)=1.14,
    nat=30,
      ntyp=2,
    ecutwfc =35.0,
      ecutrho =350.0,
      occupations= 'smearing',
    degauss= 0.03,
      smearing= 'cold',
 /
  &electrons
      mixing_beta = 0.7
    conv_thr =  1.0d-12
    diagonalization = 'cg'
/
 ATOMIC_SPECIES
  Mg 24.3 Mg.pbe-n-rrkjus.UPF
  B  10.8 B.pbe-n-rrkjus.UPF
ATOMIC_POSITIONS  {angstrom}
Mg          0.00  0.00  0.00
Mg          -0.00  -0.00  1.00
Mg          -0.00  1.00  0.00
Mg          -0.00  1.00  1.00
Mg          1.00  0.00  0.00
Mg          1.00  -0.00  1.00
Mg          1.00  1.00  0.00
Mg          1.00  1.00  1.00
B          -0.00  0.577350  0.571000
B            1.00  0.577350  0.571000
B            0.422650  0.422650  0.571000
B            0.577350  0.00  0.571000
B            0.577350  1.00  0.571000
B          -0.00  0.422650  0.571000
B            1.00  0.422650  0.571000
B            0.577350  0.577350  0.571000
B            0.422650  0.00  0.571000
B            0.422650  1.00  0.571000
B            0.50  0.288680  0.571000
B            0.711320  0.211320  0.571000
B            0.788680  0.50  0.571000
B            0.50  0.711320  0.571000
B            0.288680  0.788680  0.571000
B            0.211320  0.50  0.571000
B            0.711320  0.50  0.571000
B            0.788680  0.288680  0.571000
B            0.50  0.211320  0.571000
B            0.288680  0.50  0.571000
B            0.211320  0.711320  0.571000
B            0.50  0.788680  0.571000
K_POINTS {automatic}
18 18 9 0 0 0


With best regards,Adeniji Rasaki idowurskaden...@yahoo.com

 
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[Pw_forum] (no subject)

[tomy tunde]

Dear All,
 I tried to build a supercell with VESTA for MgB2 and I was have this error.
%%
    task #        0
    from cdiaghg : error #      129
    diagonalization (ZHEGV*) failed
 
Although, I tried to fixed the problem based on past post on this medium
but it seems to be a difficult task.

Initial, I did some electronic structure calculations base on three atomic
positions which are in agreement with previous works on it. However, the
problem started when I tried to build a supercell of 30 atoms with VESTA
in order for me to dope it with other element, I was having this error
message posted above. I will appreciate if anyone can tell me what is
wrong with my input file or how I can go about solving this particular
task. I appreciate all your kind gesture as I await your response. The
input file is given below:

&control
      calculation = 'scf'
      restart_mode='from_scratch'
      prefix='MgB2',
pseudo_dir = '/home/work/espresso-5.0/pseudo/',
    outdir='./'
/
&system
    ibrav=4,
    celldm(1)=11.66,
    celldm(3)=1.14,
    nat=30,
      ntyp=2,
    ecutwfc =35.0,
      ecutrho =350.0,
      occupations= 'smearing',
    degauss= 0.03,
      smearing= 'cold',
 /
  &electrons
      mixing_beta = 0.7
    conv_thr =  1.0d-12
    diagonalization = 'cg'
/
 ATOMIC_SPECIES
  Mg 24.3 Mg.pbe-n-rrkjus.UPF
  B  10.8 B.pbe-n-rrkjus.UPF
ATOMIC_POSITIONS  {angstrom}
Mg          0.00  0.00  0.00
Mg          -0.00  -0.00  1.00
Mg          -0.00  1.00  0.00
Mg          -0.00  1.00  1.00
Mg          1.00  0.00  0.00
Mg          1.00  -0.00  1.00
Mg          1.00  1.00  0.00
Mg          1.00  1.00  1.00
B          -0.00  0.577350  0.571000
B            1.00  0.577350  0.571000
B            0.422650  0.422650  0.571000
B            0.577350  0.00  0.571000
B            0.577350  1.00  0.571000
B          -0.00  0.422650  0.571000
B            1.00  0.422650  0.571000
B            0.577350  0.577350  0.571000
B            0.422650  0.00  0.571000
B            0.422650  1.00  0.571000
B            0.50  0.288680  0.571000
B            0.711320  0.211320  0.571000
B            0.788680  0.50  0.571000
B            0.50  0.711320  0.571000
B            0.288680  0.788680  0.571000
B            0.211320  0.50  0.571000
B            0.711320  0.50  0.571000
B            0.788680  0.288680  0.571000
B            0.50  0.211320  0.571000
B            0.288680  0.50  0.571000
B            0.211320  0.711320  0.571000
B            0.50  0.788680  0.571000
K_POINTS {automatic}
18 18 9 0 0 0


With best regards,Adeniji Rasaki idowurskaden...@yahoo.com

 
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Re: [Pw_forum] adding vacuum

[Jaret Qi]

Pascal:Do not you think z-vector will shrink till it reaches the optimal 
length?   


 On Tuesday, November 17, 2015 12:35 AM, Pascal Boulet 
 wrote:
   

 So, I think in this case you should also relax the z-axis: The system tends to 
fill the vacuum by moving atoms since it cannot adapt the cell parameter.
Pascal
Le 16 nov. 2015 à 21:49, Jaret Qi  a écrit :

To make it clear, I am not adding vacuum to isolate my system like in graphene 
where we make the z-axis large enough to make it graphene not graphite. My 
system is a (001) interface between semi-metallic and semiconductor, so i am 
trying to minimize the interaction along the interface which is along the 
z-axis and study some properties and match it with experimental results. I need 
a reasonable vacuum so I began with 4A.
 



 On Monday, November 16, 2015 1:31 PM, Nicola Marzari 
 wrote:
   

 On 16/11/2015 21:17, Jaret Qi wrote:
> but that will cost time!

you are right! just keep the 4 angstroms, no one will notice.

(actually, skip the calculations altogether, and make up some
plausible numbers in your paper - that will be even faster).

            nicola

>
>
>
> On Monday, November 16, 2015 9:26 AM, Pascal Boulet
>  wrote:
>
>
> Hello,
>
> 4 angstroms wide seems to be very small for the vacuum. As a rule of
> thumb you should use at least 2.5 times the thickness of your slab. This
> is what we observed in the calculations of semiconductor slabs. This has
> to be tested.
>
> Pascal
>
> Le 16 nov. 2015 à 16:40, Jaret Qi  > a écrit :
>
>> Hello all,
>> I am trying to minimize the interaction between my system and its
>> periodic images. To do so, I introduced a layer of vacuum along the
>> z-axis by increasing the lattice vector along the z-axis by 4A. At the
>> same time, I fixed it by using this parameter: cell_dofree='2Dxy',
>> But I have noticed atoms that are close to the vacuum move along the
>> z-axis and vacuum is decreasing, is this wrong or I should use
>> different cell_dofree?
>> note:relaxation still ongoing, not relaxed yet.
>>
>>
>> JARET,
>> ASU
>> ___
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>
> --
> Pascal Boulet /- MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE/
> Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie
> Niemen - 13013 Marseille
> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
> Site : http://allos.up.univ-mrs.fr/pascal - Email :
> pascal.bou...@univ-amu.fr 
> /Afin de respecter l'environnement, merci de n'imprimer cet email que si
> nécessaire./
>
>
>
>
>
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-- 
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project


   

--
Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIEAix-Marseille 
Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 
MarseilleTél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50Site : 
http://allos.up.univ-mrs.fr/pascal - Email : pascal.boulet@univ-amu.frAfin de 
respecter l'environnement, merci de n'imprimer cet email que si nécessaire.


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Re: [Pw_forum] Problem with visualization of pw.x output using XCrysden

[Tone Kokalj]

On Tue, 2015-11-17 at 14:19 +0100, liyinc...@gmail.com wrote:
> Dear QE community,
> 
> I encountered a strange problem with visualization of pw.x output 
> using XCrysden. I was visualizing  the final structure after geometry 
> optimization using Xcrysden. When the coordinates of atoms shown in 
> Xcrysden in the unit of crystal, they are same with those in pw.x 
> output. But after I switched the unit from crystal to alat, I found 
> those values are a little different from what were written in pw.x 
> output file.
 
There can be two reasons: if they are marginally different the reason
may be due to, say, round-off errors.

But if they differ considerably the reason is different: in xcrysden
the "alat" always refers to the length of the first Bravais lattice
vector, whereas in pw.x the "alat" is the size of celldm(1) (or A).
Hence, if you set the celldm(1) (or A) to a value different then the
size of the first Bravais lattice vector in the input, then xcrysden's
alat and pw.x alat coordinates will be different.

What is the case in your situation I cannot say, unless you provide the
pertinent output file.

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


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[Pw_forum] Problem with visualization of pw.x output using XCrysden

[liyinc...@gmail.com]

Dear QE community,

I encountered a strange problem with visualization of pw.x output using 
XCrysden. I was visualizing  the final structure after geometry optimization 
using Xcrysden. When the coordinates of atoms shown in Xcrysden in the unit of 
crystal, they are same with those in pw.x output. But after I switched the unit 
from crystal to alat, I found those values are a little different from what 
were written in pw.x output file. I first thought it may be caused by different 
calculation equations they used.  But when I was visualizing the initial 
structure, the coordinates show in the unit of alat in pw.x output is 
completely same as the those in Xcrysden.

I recognized a sentence at the end of pw.x output file before the scf 
calculation of the relaxed structure, "The G-vectors are recalculated for the 
final unit cell. Results may differ from those at the preceding step". I am not 
clear what these words mean here. Perhaps the parameters of unit cell is 
changed in the last scf calculation resulting the discrepancy between pw.x and 
Xcrysden? 

Thanks a lot for your kind help!

Best Regards,
Yin


Dr. Yin Li 
Department of Biophysics,Medical School, University of Pecs,
No.12 Szigeti Street, Pecs, H-7624, HUNGARY
Phone: +36-72-535271/36271
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[Pw_forum] Dielectric constant of ZnAl2O4:Cu

[Winfred Mulwa]

Dear all,
I would wish to calculate the dielectric constant of ZnAl2O4:Cu. I have run
the scf calculation which is the first part of optical properties. My
question is, what should i include in the input file so that i can get the
dielectric constant from -2 to 2 charges.
Kind regards
Mulwa Winfred.
D Phil Student, Computational Material Science Group,
University of the Free State - QwaQwa,
South Africa.
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