Re: [QE-users] on the use of tb09 functional from libxc

[José Carlos Conesa]

Hi,

What I could verify is that, in a simple test on rutile TiO2, I obtain 
the same total energy (to within 10**(-7) Ry) with any of these lines in 
the input file:


input_dft='sla+pw+tb09+tb09'

input_dft='pw+pbc+tb09+tb09'

input_dft="noc+nogc+tb09+tb09"

The first case is the one specified in the Modules/funct.f90 file as 
equivalent to input_dft='tb09', the second one corresponds to having gga 
correlation, the last one, to using no correlation at all. One can 
understand this since the said file contains these lines:


    ! special case : TB09 meta-GGA Exc
    else IF ('TB09'.EQ. TRIM(dftout) ) THEN
   dft_defined = set_dft_values(0,0,0,0,0,3)

I think that since the original mBJ functional was defined as including 
LDA correlation, this should be changed. Preferably, by allowing the 
user to specify the type of correlation (s)he desires. I wonder if just 
suppressing in the said file the three lines mentioned above would be 
enough.


Regards,

JC Conesa

El 05/05/2018 a las 10:44, Paolo Giannozzi escribió:
I don't think it is possible right now to use any meta-GGA with 
exchange/correlations/gradient corrections that differ from those 
assumed in the original definition of the meta-GGA functional. 
Meta-GGA follow a different path from all other XC functionals. I hope 
to manage sooner or later to clean up the meta-GGA mess, but cannot 
guarantee anything.


Paolo

On Fri, May 4, 2018 at 6:33 PM, José C. Conesa > wrote:


Hi,

Does this mean that it is not possible to combine tb09 with any
correlation contribution?

José Carlos


El 04/05/2018 a las 17:41, Paolo Giannozzi escribió:

I think that with meta-GGA what is written in the first two
fields is just ignored

Paolo

On Fri, May 4, 2018 at 5:39 PM, José C. Conesa
> wrote:

Dear QE developers,

I wish to use in Quantum Espresso the tb09 potential-only
meta-GGA functional (from Tran & Blaha, PRL 102, 2009,
226401) which is available in libxc. I downloaded the libxc
library and compiled successfully qe-6.2.1 with it. Then I
see in Modules/funct.f90 that the instruction to use this
functional is equivalent to specifying

input_dft="sla+pw+tb09+tb09"

But as far as I know, the tb09 functional gives only the
exchange part, and gives it in full (not as a correction to
another expression for the exchange), while sla is a LDA
exchange form (and pw a LDA correlation form). Should one
conclude that exchange is being introduced twice? And, is a
gradient correction to the correlation term not included?
From these considerations, I would have thought that using
something like

input_dft="pw+pbc+tb09+tb09"

(where I hope that the tb09 exchange functional is not
included twice), i.e. the correlation part of PBE plus the
Tran & Blaha exchange functional, would be the proper way to
proceed.

Can you please comment on this?

I also would add that it would be good to be able to adjust
the A and B parameters of the tb09 functional. This has been
proposed in (Koller, Tran & Blaha, PRB 85, 2012, 155109) to
obtain better bandgaps in certain families of semiconductors.

All the best,

-- 
José C. Conesa

Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie 2, Cantoblanco
28049 Madrid, Spain
Tel. (+34)915854766




Libre de virus. www.avast.com





<#m_3291306830783023308_m_5099655024476259839_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy


Phone +39-0432-558216, fax +39-0432-558222



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-- 
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Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie 2, Cantoblanco
28049 Madrid, 

[QE-users] Strange phonons frequencies with spin included

[Qiyuan Ruan]

Dear developers,
Recently I was trying phonon calculations with spin, and was getting strange 
results, so I went down to one carbon atom in vacuum expecting frequencies to 
be close to zero. However, it seems that results vary a lot giving frequency 
-51 cm^-1 for C.pz-n-kjpaw_psl.0.1.UPF pseudopotential, and ~900-1000 cm^-1 
with C.pbe-van_bm.UPF pseudopotential. Otherwise the calculation seems to be 
running fine, so there is no way of knowing if there is a problem or not. I am 
using version 6.0 and including my inputs and excerpts from output. Kindly 
please help me resolve this if you have any insights. Thank you!

Qiyuan Ruan


SCF input:
scf.in

calculation='scf'
etot_conv_thr = 1.d-11,
verbosity='high',
/
 
nat=1, ntyp=1,
ibrav=0,
ecutwfc=60.0, occupations='smearing', degauss = 0.01, smearing='mp',
la2F = .true.,
nspin = 2,
starting_magnetization(1) = 1,
nosym =.true.,
 /
 
mixing_beta = 0.5,
mixing_mode = 'local-TF'
conv_thr =  1.0d-12,
 /
ATOMIC_SPECIES
 C  12.01 C.pz-n-kjpaw_psl.0.1.UPF
CELL_PARAMETERS  angstrom
10.000 0.000 0.000
0.000 10.000 0.000
0.000 0.000 10.000
ATOMIC_POSITIONS crystal
C 0.5 0.5 0.5
K_POINTS automatic
1 1 1 0 0 0

Phonon input:


  tr2_ph=1.0d-17,
  alpha_mix(1)=0.3,
  amass(1)=12.01,
  niter_ph=500,
  trans=.true.,
  ldisp=.true.,
  nq1=1, nq2=1, nq3=1,
  start_q=1,
  last_q=1,
 /

Output for C.pz-n-kjpaw_psl.0.1.UPF:

Diagonalizing the dynamical matrix

 q = (0.0   0.0   0.0 )

 **
 freq (1) =  -1.543361 [THz] = -51.480967 [cm-1]
 freq (2) =  -1.540965 [THz] = -51.401048 [cm-1]
 freq (3) =  -1.538275 [THz] = -51.311315 [cm-1]
***
Output for C.pbe-van_bm.UPF:

Diagonalizing the dynamical matrix

 q = (0.0   0.0   0.0 )

 **
 freq (1) =  26.838049 [THz] = 895.220954 [cm-1]
 freq (2) =  30.156019 [THz] =1005.896529 [cm-1]
 freq (3) =  30.677843 [THz] =1023.302678 [cm-1]
 **


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[QE-users] final scf stuck in first iteration and relaxed hexagonal cell parameters changes abnormally

[Dr. K. C. Bhamu]

Dear Users,

I have three queries as mentioned below:

Query-1

I am relaxing (vc-relax and vc-relax with cell_dofree=xyz) the hybrid
perovskite structure. In both, the case the vc-relax goes well and prints
final relaxed ordinates (End final coordinates
).
As in the newest QE version, 6.2.1, the pw.x run a final scf at the
vc-relaxed structure.

In my case, the final scf starts but it always stuck at the first iteration:



iteration #  1 ecut=50.00 Ry beta= 0.70
 Davidson diagonalization with overlap



Could you please help me to figure out the issue why it stuck and what
should I do so that the final scf ends without any error.



Query-2


My structure is hexagonal with the initial cell dimensions;

  celldm(1)=16.1636080003d0, celldm(3)=1.3049995364d0,

or

 a= 8.56909772473  b= 8.57159817464  c= 11.2622477409Vol.=
716.067118376, c/a= 1.31428629976;  alpha= 90.0   beta= 90.0   gamma=
120.045402959


after vc-relax I am getting the final cell parameters as below:


a= 8.71101209853  b= 8.85373809923  c= 11.4881609903Vol.=
750.696449907,   c/a= 1.31880898113'   alpha= 86.512834873   beta=
92.9705116854   gamma= 121.889941369

you see here that the a and b are slightly different while in the hexagonal
system they should be same. Also the alpha, beta and gamma are also not at
90, 90 and 120 as supposed to remain at this value in the hexagonal system.


To overcome this issue, I have done another vc-relax with "cell_dofree=xyz"
to keep fix the lattice angles) I am getting the final cell parameters as
below:


AA a= 8.87533777693  b= 8.52082228214  c= 11.6157398387Vol.=
753.329940336,c/a= 1.30876594566 ;  alpha= 90.0   beta= 90.0   gamma=
120.954649993

Again we see the variation in the cell parameters. However, the variation
is small in comparison to pure vc-relax and alpha and beta are now at fix
value.


Could you please tell me why I am getting this variation in the cell
parameters?



Quer-3


If possible, please also cover my previous post which is here:

https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33935.html



with kind regards


K.C. Bhamu
CSIR-NCL, Pune, India
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Re: [QE-users] users Digest, Vol 130, Issue 15

[Hanuma Kumar]

Dear Giovanni Cantele

Thank you


with regards

Hanuma Kumar

On Wed, May 16, 2018 at 3:30 PM, <users-requ...@lists.quantum-espresso.org>
wrote:

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> Today's Topics:
>
>1. Which celldm(i) to choose for DOS (Sudip Kumar Mondal)
>2. Reg: need of Antimony (Sb) Ultrasoft Pseudopotentials
>   (Hanuma Kumar)
>3. Re: Which celldm(i) to choose for DOS (Giovanni Cantele)
>4. Re: Reg: need of Antimony (Sb) Ultrasoft Pseudopotentials
>   (Giovanni Cantele)
>
>
> --
>
> Message: 1
> Date: Wed, 16 May 2018 12:55:07 +0530
> From: Sudip Kumar Mondal <sudipkm1...@gmail.com>
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] Which celldm(i) to choose for DOS
> Message-ID:
> <CA+=N5Lvrgb4GyT=5vJe9fzYRUAtwxN4MMG=VuCXC7jKUK
> xu...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all ,
>
> I'm currently using QE 5.4.0. & I have a general question regarding the
> calculation of density of states (LDOS & PDOS).
>
> Before estimating any physical observable we optimize (relax/vc-relax or
> sometimes both) the structure in hand to obtain accurate lattice
> parameter(s) corresponding to zero kBar pressure. Optimizations w.r.t. all
> other parameters (k-point grid , ecutwfc , ecutrho etc.)  are also
> performed.
> However for a single scf run with the lattice parameter(s) corresponding to
> zero pressure as obtained from relax/vc-relax , yields some different
> pressure other than zero kBar.  In my case then I ran a series of single
> scf calculations for converging to zero pressure by varying the lattice
> parameter. The scf convergence to zero pressure was successful. But the
> lattice parameter  turned out be smaller than its zero pressure equivalent
> obtained from relaxation by ~ 0.9 bohr.
>
> Now, my question is whether I should proceed to calculate DOS with the
> value of the lattice parameter(s) corresponding to zero pressure obtained
> from relaxation or with the same obtained from the series of single scfs?
>
>
> Regards.
> --
> Sudip Kumar Mondal
> DST INSPIRE Fellow
> High Pressure & Temperature Laboratory
> Dept. Of Physics/Geological Sc.
> Jadavpur University.
> -- next part --
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>
> --
>
> Message: 2
> Date: Wed, 16 May 2018 13:24:33 +0530
> From: Hanuma Kumar <hanuma...@gmail.com>
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] Reg: need of Antimony (Sb) Ultrasoft
> Pseudopotentials
> Message-ID:
> <CA+M8iEdCDiNp4U0cqYfjUr4BQv91M7Dkizqap-3r8emeQ8pS=Q@mail.gmail.
> com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Quantum Espresso users,
>
> I have calculated band structure of Sb (Antimony) based intermetallics, and
> I have calculated band structure of the alloys using NORMCONS
> Pseudopotentials. The density of states and band structure is matches with
> the reported results, but their magnetic moments are not matching. In order
> to get good results, I am interested to do with Ultrasoft pseudopotentials.
> These type of pseudopotentials is not available for Sb (Antimonty, Atomic
> number 51) and I don't know how to generate pseudopotentials. If possible,
> can anyone please send me the USPP files for Sb.
>
>
> Thanks and regards
>
> Hanuma.
> -- next part --
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> --
>
> Message: 3
> Date: Wed, 16 May 2018 10:05:55 +0200
> From: Giovanni Cantele <giovanni.cant...@spin.cnr.it>
> To: Quantum Espresso users Forum <users@lists.quantum-espresso.org>
> Subject: Re: [QE-users] Which celldm(i) to choose for DOS
> Message-ID: <3896547b-f251-45f2-80c5-1385f53ab...@spin.cnr.it>
> Content-Type: text/p

Re: [QE-users] Band Structure and DOS contradiction

[Giovanni Cantele]

Maybe you could send input files and a plot of DOS and band structure to help 
people to figure out
what is happening.

If DOS and band structure do not agree with each other, I would not trust to 
either!!!

What do you mean that you repeat the calculation with **different theory** 

Giovanni



> On 16 May 2018, at 13:17, B S Bhushan  wrote:
> 
> Dear Experts,
> 
> I am analyzing defected graphene with different dopants.
> In very few cases... I end up having contradictory DOS and Band structure.
> 
> The Band structure shows a small band gap at the fermi level, however, the 
> DOS shows states on the fermi level.
> Same result appears even if the calculation is repeated with different theory.
> In such cases, Should I depend on the Band structure or the DOS.
> What should I call the system, metallic or semi-metallic or semi-conducting 
> ???
> 
> Please suggest.
> 
> 
> Sincerely,
> B S Bhushan,
> Ph.D Scholar,
> ABV- Indian Institute of Information Technology and Management, Gwalior.
> www.bsbhushan.com 
> 
> 
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-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.fisica.unina.it/~cantele

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[QE-users] Band Structure and DOS contradiction

[B S Bhushan]

 Dear Experts,

I am analyzing defected graphene with different dopants.
In very few cases... I end up having contradictory DOS and Band structure.

The Band structure shows a small band gap at the fermi level, however, the
DOS shows states on the fermi level.
Same result appears even if the calculation is repeated with different
theory.
In such cases, Should I depend on the Band structure or the DOS.
What should I call the system, *metallic *or* semi-metallic *or*
semi-conducting *???

Please suggest.


Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com
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Re: [QE-users] Reg: need of Antimony (Sb) Ultrasoft Pseudopotentials

[Giovanni Cantele]

Actually, US pseudo potential for Sb is downloadable at the Pseudopotentials 
page of Quantum-espresso
http://www.quantum-espresso.org/pseudopotentials/ps-library/sb 


The files you find are built using pslibrary:
https://dalcorso.github.io/pslibrary/ 


> On 16 May 2018, at 09:54, Hanuma Kumar  wrote:
> 
> Dear Quantum Espresso users,
> 
> I have calculated band structure of Sb (Antimony) based intermetallics, and I 
> have calculated band structure of the alloys using NORMCONS Pseudopotentials. 
> The density of states and band structure is matches with the reported 
> results, but their magnetic moments are not matching. In order to get good 
> results, I am interested to do with Ultrasoft pseudopotentials. These type of 
> pseudopotentials is not available for Sb (Antimonty, Atomic number 51) and I 
> don't know how to generate pseudopotentials. If possible, can anyone please 
> send me the USPP files for Sb.
> 
> 
> Thanks and regards
> 
> Hanuma.
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-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.fisica.unina.it/~cantele

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Re: [QE-users] Which celldm(i) to choose for DOS

[Giovanni Cantele]

Dear Sudip,

I’m not sure I’ve fully understood your question. You are saying that, after a 
vc-relax calculation, you use the final output lattice parameter(s) in a single 
scf run,
and you obtain a different pressure, aren’t you?

As far as I remember, during vc-relax the code uses a fixed number of plane 
waves (because it cannot change the basis set during a single calculation).
On the other hand, in a single scf run the number of plane waves depends on the 
lattice parameter. So, it might happen that the basis set of the scf run is 
different from
that of the vc-relax run, because the latter is setup based on the initial 
cell, and not the last one that is unknown. So maybe you could compare the two 
basis sets, and then
try to make for example the scf run with the vc-relax basis set, in place of 
the default one, just to check that you obtain exactly the same results. In any 
case, I think that if this is 
the case the differences you experience in the lattice parameter should be 
negligible or small.

Giovanni

PS by the way, after writing this message I’ve find the FAQ addressing just you 
issue!
http://www.quantum-espresso.org/resources/faq/self-consistency#6.11

> On 16 May 2018, at 09:25, Sudip Kumar Mondal  wrote:
> 
> Hi all ,
>  
> I'm currently using QE 5.4.0. & I have a general question regarding the 
> calculation of density of states (LDOS & PDOS).
> 
> Before estimating any physical observable we optimize (relax/vc-relax or 
> sometimes both) the structure in hand to obtain accurate lattice parameter(s) 
> corresponding to zero kBar pressure. Optimizations w.r.t. all other 
> parameters (k-point grid , ecutwfc , ecutrho etc.)  are also performed.
> However for a single scf run with the lattice parameter(s) corresponding to 
> zero pressure as obtained from relax/vc-relax , yields some different 
> pressure other than zero kBar.  In my case then I ran a series of single scf 
> calculations for converging to zero pressure by varying the lattice 
> parameter. The scf convergence to zero pressure was successful. But the 
> lattice parameter  turned out be smaller than its zero pressure equivalent 
> obtained from relaxation by ~ 0.9 bohr.
> 
> Now, my question is whether I should proceed to calculate DOS with the value 
> of the lattice parameter(s) corresponding to zero pressure obtained from 
> relaxation or with the same obtained from the series of single scfs?
> 
> 
> Regards.
> -- 
> Sudip Kumar Mondal
> DST INSPIRE Fellow
> High Pressure & Temperature Laboratory
> Dept. Of Physics/Geological Sc.
> Jadavpur University.
> ___
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> users@lists.quantum-espresso.org
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-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.fisica.unina.it/~cantele

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[QE-users] Reg: need of Antimony (Sb) Ultrasoft Pseudopotentials

[Hanuma Kumar]

Dear Quantum Espresso users,

I have calculated band structure of Sb (Antimony) based intermetallics, and
I have calculated band structure of the alloys using NORMCONS
Pseudopotentials. The density of states and band structure is matches with
the reported results, but their magnetic moments are not matching. In order
to get good results, I am interested to do with Ultrasoft pseudopotentials.
These type of pseudopotentials is not available for Sb (Antimonty, Atomic
number 51) and I don't know how to generate pseudopotentials. If possible,
can anyone please send me the USPP files for Sb.


Thanks and regards

Hanuma.
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[QE-users] Which celldm(i) to choose for DOS

[Sudip Kumar Mondal]

Hi all ,

I'm currently using QE 5.4.0. & I have a general question regarding the
calculation of density of states (LDOS & PDOS).

Before estimating any physical observable we optimize (relax/vc-relax or
sometimes both) the structure in hand to obtain accurate lattice
parameter(s) corresponding to zero kBar pressure. Optimizations w.r.t. all
other parameters (k-point grid , ecutwfc , ecutrho etc.)  are also
performed.
However for a single scf run with the lattice parameter(s) corresponding to
zero pressure as obtained from relax/vc-relax , yields some different
pressure other than zero kBar.  In my case then I ran a series of single
scf calculations for converging to zero pressure by varying the lattice
parameter. The scf convergence to zero pressure was successful. But the
lattice parameter  turned out be smaller than its zero pressure equivalent
obtained from relaxation by ~ 0.9 bohr.

Now, my question is whether I should proceed to calculate DOS with the
value of the lattice parameter(s) corresponding to zero pressure obtained
from relaxation or with the same obtained from the series of single scfs?


Regards.
-- 
Sudip Kumar Mondal
DST INSPIRE Fellow
High Pressure & Temperature Laboratory
Dept. Of Physics/Geological Sc.
Jadavpur University.
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