[Pw_forum] GW for graphene

[Andrea Pedrielli]

Dear users,
we are doing some GW calculation with Quantum Espresso, version 6.1. Our
interest is to compute the GW correction to DFT for high energy states. We
are using the GWL code with C.pbe-mt_fhi.UPF pseudopotential. We are facing
some difficulties, in particular when we plot the GW correction to DFT we
find some spikes (see attached image) that seem to be very unphysical
(corrections of the order of 5 eV ) and depends in a sensitive manner from
the parameters used in the simulations, but the presence of which is a
constant largely independently from the unit cell, the number of bands etc.
In general we are taking as reference this paper https://arxiv.org/pdf/
0806.3365.pdf , in which the GW band structure presents differences with
DFT one smaller than 5 eV at the Gamma point.

I would ask you some questions, the first of them whether some of you see
whatever clear error in our input files (that I attach below).

1) What could be conservative parameters for the graphene cell? In
particular, in the various tutorials on GWL is reported that the number of
atoms (8) for the Silicon example is too small "use at least 64 atoms cells
for production calculations". We tried with a 8 and 18 atoms unit cell and
the spikes in the GW correction remain.  Is the cell dimension a
fundamental parameter, due to the Gamma point GW calculation, though it is
sampled with a fine k point grid?

2) From the working experience with the code seems to be some relations
between the  ecutwfc (kinetic energy cutoff  for wavefunctions)   and
numw_prod (length of the polarizability basis), is it true? In particular
with small ecutwfc we found problems in increasing  numw_prod

3) What could be a reasonable starting point for numw_prod? Until now we
played with this parameter around a value of 100-200, but could it be a too
small value? In the GWL manual is reported that numw_prod scales linearly
with respect to the dimensions of the system, but is there a typical
relation? In the examples it is set to 100 for both Silicon and CH4, but
for 72 atoms (that could be a largely conservative unit cell for graphene)
should be 500, 1000, 2000?


If someone has any idea on the way to go forward, is very welcome.

Thanks in advance,

Andrea Pedrielli

FBK-ECT* Trento


1-Gsingle_scf0.inp
Description: Binary data


2-Gsingle_head0.inp
Description: Binary data


3-Gsingle_nscf0.inp
Description: Binary data


4-Gsingle_pw4gww0.inp
Description: Binary data


5-Gsingle_gww0.inp
Description: Binary data


Gsingle_scf0en-50-fhi-df2-c09-bands.dat1
Description: Binary data
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Re: [Pw_forum] QE 6.1 Error

[Paolo Giannozzi]

As a strict minimum, one needs to know
- how the code is compiled and run: serial, parallel,  ...
- the data needed to reproduce the problem

Paolo

On Mon, Jul 3, 2017 at 5:34 PM, Manu Hegde  wrote:

> Hello,
>
> I am using QE 6.1, it is doing fine with pw.x calculations, whenever i use
> plotting utilities like bands.x or projwfc.x i am getting following error,
>
> Image  PCRoutineLineSource
> projwfc.x  0083872A  Unknown   Unknown  Unknown
> projwfc.x  0064C8D5  Unknown   Unknown  Unknown
> projwfc.x  00645BAF  Unknown   Unknown  Unknown
> projwfc.x  004BEA60  Unknown   Unknown  Unknown
> projwfc.x  004BD50E  Unknown   Unknown  Unknown
> projwfc.x  004BCE0E  Unknown   Unknown  Unknown
> projwfc.x  00449FBF  Unknown   Unknown  Unknown
> projwfc.x  0044910C  Unknown   Unknown  Unknown
> libc.so.6  7F3BA10BAD5D  Unknown   Unknown  Unknown
> projwfc.x  00449009  Unknown   Unknown  Unknown
>
> [gb35][[27039,1],1][../../../../../../../openmpi-1.6.2/ompi/
> mca/btl/tcp/btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> [gb29][[27039,1],2][../../../../../../../openmpi-1.6.$
> [gb29][[27039,1],4][../../../../../../../openmpi-1.6.2/ompi/
> mca/btl/tcp/btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset$
>
>
> Thanks,
> Manu
> (University of Waterloo)
>
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] nscf related problem

[Lorenzo Paulatto]

Dear Anindya,
you are using more pools than there are k-points. As pools are 
parallelization over k-points, this is not possible. Either use less 
pools or more k-points

On 04/07/17 13:11, Anindya Bose wrote:
> Dear Sir,
> While performing nscf calculation using 64 processor(parallelization) , 
> I am getting this error.I don't know how this is happening.
> 
> Error in routine divide_et_impera (1):
>some nodes have no k-points
> 
> Please help me to solve this.
> 
> Thanks and regards,
> 
> Anindya Bose
> 
> Research Feloow,
> 
> Indian Institute of Information Technology,Allahabad
> 
> 
> 
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IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
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[Pw_forum] Water confinement

[Ubaid Mohd]

Dear all,
I am doing the calculations of water confinement between graphene sheets. I
have done all the relaxation calculations. After relaxation I found the
total energy of the graphene sheet, I also need  to find the total energy
of the water molecule to get the total binding energy of the system.
My question is, to find the total energy of the water molecule what should
be the crystal structure of water and how I create the unit cell of water.
Thanks in advance.

*Mohammad Ubaid*
*PhD Research Scholar*
*Department of Physics*
*Jamia Millia Islamia University*
*New Delhi - 110025*
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Re: [Pw_forum] Need help in spin polarized calculations

[sayan chaudhuri]

Dear QE experts,

Thank you, sir, for the suggestion. I will follow the same.
I tried tot_magnetization along with smearing and varied tot_magnetization
to achieve the lowest total energy. And this optimization is giving the
same value of tot_magnetization as expected from slater-pauling rule. Is
this procedure is wrong?

Thanking you,
   Sayan Chaudhuri


On Tue, Jul 4, 2017 at 1:46 PM, Mostafa Youssef  wrote:

> Dear Sayan,
>
> In the case of metallic systems, it is recommended to use smearing. With
> the smearing applied, you can use start_magnetization to give an initial
> guess for the magnetic moment.  pw.x will try self-consistently to find the
> final magnetization that leads to minimum energy (Achieving both goals
> simultaneously).  No need for the tot_magnetization in this case.
>
>
> Regards,
> Mostafa
>
>
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[Pw_forum] nscf related problem

[Anindya Bose]

Dear Sir,
While performing nscf calculation using 64 processor(parallelization) , I
am getting this error.I don't know how this is happening.

Error in routine divide_et_impera (1):
  some nodes have no k-points

Please help me to solve this.

Thanks and regards,

Anindya Bose

Research Feloow,

Indian Institute of Information Technology,Allahabad
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Re: [Pw_forum] (no subject)

[Paolo Giannozzi]

>From the header of next version of average.f90:

  !  The planar average is defined as
  ! p(k) = \sum_{i=1}^{N_1} \sum_{j=1}^{N_2} Q(i,j,k) / (N_1 N_2)
  !  along direction 3, and the like for directions 1 and 2;
  !  N_1, N_2, N_3 are the three dimensions of the 3D FFT.
  !  Note that if Q is a charge density whose integral is Z_v:
  ! Z_v = \int p(z) dV = \sum_k p(k) \Omega/N_3
  !  where \Omega is the size of the unit cell (or supercell)

P.

On Tue, Jul 4, 2017 at 12:02 PM, VineetKumar Pandey <
vineetkumar.pan...@students.iiserpune.ac.in> wrote:

> dear sir, when we do average.x, we get charge per unit surface, I want to
> know unit of charge , I mean it's in electronic unit or coulomb. and sir I
> multiplied it by area. it's coming half of the charge in comparison with
> what it should be.
>
>
> thank you
>
> Vineet Kumar Pandey
> IISER PUNE, INDIA
> PINCODE-411008
>
> Phone: +91 8853094275 <+91%2088530%2094275>
>
>
> On Tue, Jul 4, 2017 at 2:49 PM, Thomas Brumme <
> thomas.bru...@uni-leipzig.de> wrote:
>
>> Dear Vineet Kumar,
>>
>> if you average the charge over a surface you'll get the charge per unit
>> surface. Integrating this will give you the total charge per unit surface...
>>
>> I think the output of average.x is just this... Thus, you'll need to
>> multiply by the xy-area of your unit cell...
>>
>> Regards
>>
>> Thomas
>>
>> On 07/04/17 11:08, VineetKumar Pandey wrote:
>>
>> I am trying to calculate charge density(rho)  as a function of z axis.
>> what I did by using pp.x and then average.x. but when I am integrating
>> rho(z)  with respect to z. I am not getting the total charge, that I have
>> in my system. can anybody help me to get out of it?  actually, my system is
>> PbI2. and it has 18 e- in a unit cell.
>> Vineet Kumar Pandey
>> IISER PUNE, INDIA
>> PINCODE-411008
>>
>> Phone: +91 8853094275 <+91%2088530%2094275>
>>
>>
>>
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>>
>>
>> --
>> Dr. rer. nat. Thomas Brumme
>> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
>> Leipzig University
>> Phillipp-Rosenthal-Strasse 31
>> 04103 Leipzig
>>
>> Tel:  +49 (0)341 97 36456 <+49%20341%209736456>
>>
>> email: thomas.bru...@uni-leipzig.de
>>
>>
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>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] (no subject)

[VineetKumar Pandey]

dear sir, when we do average.x, we get charge per unit surface, I want to
know unit of charge , I mean it's in electronic unit or coulomb. and sir I
multiplied it by area. it's coming half of the charge in comparison with
what it should be.


thank you

Vineet Kumar Pandey
IISER PUNE, INDIA
PINCODE-411008

Phone: +91 8853094275


On Tue, Jul 4, 2017 at 2:49 PM, Thomas Brumme 
wrote:

> Dear Vineet Kumar,
>
> if you average the charge over a surface you'll get the charge per unit
> surface. Integrating this will give you the total charge per unit surface...
>
> I think the output of average.x is just this... Thus, you'll need to
> multiply by the xy-area of your unit cell...
>
> Regards
>
> Thomas
>
> On 07/04/17 11:08, VineetKumar Pandey wrote:
>
> I am trying to calculate charge density(rho)  as a function of z axis.
> what I did by using pp.x and then average.x. but when I am integrating
> rho(z)  with respect to z. I am not getting the total charge, that I have
> in my system. can anybody help me to get out of it?  actually, my system is
> PbI2. and it has 18 e- in a unit cell.
> Vineet Kumar Pandey
> IISER PUNE, INDIA
> PINCODE-411008
>
> Phone: +91 8853094275
>
>
>
> ___
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> listPw_forum@pwscf.orghttp://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
> Dr. rer. nat. Thomas Brumme
> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
> Leipzig University
> Phillipp-Rosenthal-Strasse 31
> 04103 Leipzig
>
> Tel:  +49 (0)341 97 36456
>
> email: thomas.bru...@uni-leipzig.de
>
>
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Re: [Pw_forum] (no subject)

[Thomas Brumme]

Dear Vineet Kumar,

if you average the charge over a surface you'll get the charge per unit 
surface. Integrating this will give you the total charge per unit surface...


I think the output of average.x is just this... Thus, you'll need to 
multiply by the xy-area of your unit cell...


Regards

Thomas


On 07/04/17 11:08, VineetKumar Pandey wrote:
I am trying to calculate charge density(rho)  as a function of z axis. 
what I did by using pp.x and then average.x. but when I am integrating 
rho(z)  with respect to z. I am not getting the total charge, that I 
have in my system. can anybody help me to get out of it?  actually, my 
system is PbI2. and it has 18 e- in a unit cell.

Vineet Kumar Pandey
IISER PUNE, INDIA
PINCODE-411008

Phone: +91 8853094275



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--
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig

Tel:  +49 (0)341 97 36456

email: thomas.bru...@uni-leipzig.de

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Re: [Pw_forum] (no subject)

[Giovanni Cantele]

Because the planar average is defined as the planar integral divided by the 
in-plane unit cell area, maybe you are getting the total charge divided by this 
area. Try to multiply your result by this area (maybe in a.u.^2) and see what 
happens

Giovanni


> On 4 Jul 2017, at 11:08, VineetKumar Pandey 
>  wrote:
> 
> I am trying to calculate charge density(rho)  as a function of z axis. what I 
> did by using pp.x and then average.x. but when I am integrating rho(z)  with 
> respect to z. I am not getting the total charge, that I have in my system. 
> can anybody help me to get out of it?  actually, my system is PbI2. and it 
> has 18 e- in a unit cell. 
> Vineet Kumar Pandey
> IISER PUNE, INDIA
> PINCODE-411008
> 
> Phone: +91 8853094275
> 
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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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[Pw_forum] (no subject)

[VineetKumar Pandey]

I am trying to calculate charge density(rho)  as a function of z axis. what
I did by using pp.x and then average.x. but when I am integrating rho(z)
with respect to z. I am not getting the total charge, that I have in my
system. can anybody help me to get out of it?  actually, my system is PbI2.
and it has 18 e- in a unit cell.
Vineet Kumar Pandey
IISER PUNE, INDIA
PINCODE-411008

Phone: +91 8853094275
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Re: [Pw_forum] Need help in spin polarized calculations

[Mostafa Youssef]

Dear Sayan,

In the case of metallic systems, it is recommended to use smearing. With the 
smearing applied, you can use start_magnetization to give an initial guess for 
the magnetic moment.  pw.x will try self-consistently to find the final 
magnetization that leads to minimum energy (Achieving both goals 
simultaneously).  No need for the tot_magnetization in this case.


Regards,
Mostafa

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Re: [Pw_forum] Regarding error during adsorption of bromine in graphene

[nipesh dulal]

Thank you sir.we will inform if anything same happens.

With Regards
Nipesh Dulal
Tribhuwan, university
Kathmandu, Nepal


On Mon, Jul 3, 2017 at 1:08 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> WHen using ultrasoft pseudopotentials (as you do), this error may
> indicate that the atoms got much closer to each other than they should.
> You can try to check the last relaxed positions with xcrysden or, put
> them back in an input file and use dist.x, to verify that nothing is
> suspect.
>
> hth
>
> On 03/07/17 06:05, nipesh dulal wrote:
> > Dear QE experts
> >
> > i am doing adsorption of bromine in 3*3 graphene sheet. But there comes
> > an error after one scf cycle which is mentioned below,
> >
> >
> >
> > Writing output data file bromine_relax_pb.save
> >   NEW-OLD atomic charge density approx. for the potential
> >
> >   negative rho (up, down):  1.894E-04 0.000E+00
> >
> >   total cpu time spent up to now is 3015.2 secs
> >
> >   per-process dynamical memory:   765.2 Mb
> >
> >   Self-consistent Calculation
> >
> >   iteration #  1 ecut=45.00 Ry beta=0.60
> >   Davidson diagonalization with overlap
> >
> >
> >   Error in routine cdiaghg (332):
> >   S matrix not positive definite
> >
> >
> >   stopping ...
> >
> > Here is the input file i have used
> >
> > 
> > calculation='relax'
> > restart_mode='from_scratch'
> > prefix='bromine_relax_pb'
> > outdir='/home/physics/Downloads/graphene/bromine',
> > pseudo_dir = '/home/physics/Downloads/graphene/pseudopotentials',
> > tstress=.true.
> > tprnfor=.true.
> > verbosity='high'
> > forc_conv_thr=1.0d-3
> > etot_conv_thr=1.0d-4
> > /
> > 
> > ibrav=4
> > celldm(1)=13.95
> > celldm(3)=2.71
> > nat=20
> > ntyp=2
> > ecutwfc=45.0
> > ecutrho=450
> > occupations='smearing'
> > smearing='mv'
> > degauss=0.002
> > vdw_corr='dft-d'
> > /
> > 
> > diagonalization='david'
> > mixing_mode='plain'
> > electron_maxstep = 100
> > mixing_beta=0.6
> > conv_thr = 1.0D-8
> > /
> > 
> > ion_dynamics='bfgs'
> > /
> >
> > ATOMIC_SPECIES
> > C 12.011 C.pbe-rrkjus.UPF
> > Br 79.90 Br.pbe-n-rrkjus_psl.0.2.UPF
> > ATOMIC_POSITIONS (angstrom)
> > C  0.001428319  -0.002221684   0.0
> > C  1.231420386   0.708643125   0.0
> > C  2.46214  -0.002217662   0.0
> > C  3.692093444   0.708644819   0.0
> > C  -1.228907612  2.128792409   0.0
> > C  0.001083491   2.839646136   0.0
> > C  1.231766190   2.128786536   0.0
> > C  2.461756350   2.839644042   0.0
> > C  4.922778865  -0.002223457   0.0
> > C  6.152768802   0.708640258   0.0
> > C  3.692440675   2.128788864   0.0
> > C  4.922431282   2.839647087   0.0
> > C  -2.459244768  4.259790447   0.0
> > C  -1.229251320  4.970648411   0.0
> > C  0.001427750   4.259792429   0.0
> > C  1.231421212   4.970653053   0.0
> > C  2.462102410   4.259795383   0.0
> > C  3.692093014   4.970654542   0.0
> > Br 2.461756350   2.558726619   3.5
> > Br 2.461756350   0.278726619   3.5
> >
> > K_POINTS {automatic}
> > 5 5 1 0 0 0
> >
> >
> > With Best Regards
> > Nipesh Dulal
> > Tribhuwan University
> > Kathmandu , Nepal
> >
> >
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>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 442 79822 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
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