[Pw_forum] Charge Density

[Mohamad Moadeli]

Dear all,

To show interface dipoles, I am trying to calculate charge density for a 2D
combined system containing Ag adsorbed on graphene sheet, like what is done
in a sample attached (rho_tot). The vacuum space is provided along the z
axis. Is it right to do the following steps?

1- Running a SCF

2- Performing a PP calculation:
&inputpp
  plot_num=0,
&plot
  nfile=1
  filepp(1)='sys.charge'
  iflag=2,
  output_format=3,
  e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
  e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
  x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
  nx=40, ny=40
  fileout='sys.charge001.dat'
 /



What if I set  iflag=3,  and finally run average.x ?

Any help will be greatly appreciated.

Best,

Mohammad,

Shahid Chamran University of Ahvaz
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Re: [Pw_forum] HSE with USPP

[Xiaoming Wang]

Thanks, it works.

 

Best,

 

Xiaoming Wang

 

IAMDN, Rutgers

 

From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Paolo Giannozzi
Sent: Friday, July 3, 2015 8:41 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] HSE with USPP

 

There is actually a stupid bug in the computation of the maximum number of 
plane waves (only for hybrid functionals and ultrasoft PPs). Please replace 
routine exx_n_plane_waves in file PW/src/exx.f90 with the attached one, report 
if it doesn't work

Paolo

 

On Wed, Jul 1, 2015 at 9:52 PM, Xiaoming Wang mailto:xw...@rci.rutgers.edu> > wrote:

Hello qe users and developers,

 

I am trying the new feature as in QE-5.2.0, which implement USPP with hybrid 
functional calculations. However, as for my calculations, I found errors in 
output which depend on number of cores I used.  The error reads “ Error in 
routine gk_sort (1):  array gk out-of-bounds” when I use 16 cores as ‘mpirun 
–np 16 pw.x’, but it works for 4 cores. However, for NCPP, I found no such 
problems, at least for my system. Does anyone know what the problem is? And the 
following is my input:

--

&control

calculation = 'scf'

restart_mode='from_scratch',

prefix='bp',

tstress = .true.

tprnfor = .true.

etot_conv_thr = 1.0D-6

forc_conv_thr = 1.0D-4

pseudo_dir = ' /pseudo',

outdir='./tmp'

wf_collect=.true.

/

&system

ibrav=8

a=3.33826

b=4.59076

c=13.0

nat=4

ntyp=1

ecutwfc=30

ecutrho=200

occupations='fixed'

nosym=.true.

noinv = .true.

input_dft = 'HSE'

nqx1=5, nqx2=4, nqx3=1

/

&electrons

diagonalization='david'

mixing_mode = 'plain'

mixing_beta = 0.7

conv_thr =  1.0d-8

/

ATOMIC_SPECIES

P  30.9738  p_pbe_v1.uspp.F.UPF

K_POINTS automatic

10 8 1 0 0 0

ATOMIC_POSITIONS (crystal)

P   0.50  0.914274  0.002447

P   0.00  0.585727  0.002447

P   0.00  0.414273  0.167618

P   0.50  0.085726  0.167617

-

 

Best,

 

Xiaoming Wang

 

IAMDN, Rutgers


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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] HSE with USPP

[Paolo Giannozzi]

There is actually a stupid bug in the computation of the maximum number of
plane waves (only for hybrid functionals and ultrasoft PPs). Please replace
routine exx_n_plane_waves in file PW/src/exx.f90 with the attached one,
report if it doesn't work

Paolo

On Wed, Jul 1, 2015 at 9:52 PM, Xiaoming Wang  wrote:

> Hello qe users and developers,
>
>
>
> I am trying the new feature as in QE-5.2.0, which implement USPP with
> hybrid functional calculations. However, as for my calculations, I found
> errors in output which depend on number of cores I used.  The error reads “
> Error in routine gk_sort (1):  array gk out-of-bounds” when I use 16 cores
> as ‘mpirun –np 16 pw.x’, but it works for 4 cores. However, for NCPP, I
> found no such problems, at least for my system. Does anyone know what the
> problem is? And the following is my input:
>
>
> --
>
> &control
>
> calculation = 'scf'
>
> restart_mode='from_scratch',
>
> prefix='bp',
>
> tstress = .true.
>
> tprnfor = .true.
>
> etot_conv_thr = 1.0D-6
>
> forc_conv_thr = 1.0D-4
>
> pseudo_dir = ' /pseudo',
>
> outdir='./tmp'
>
> wf_collect=.true.
>
> /
>
> &system
>
> ibrav=8
>
> a=3.33826
>
> b=4.59076
>
> c=13.0
>
> nat=4
>
> ntyp=1
>
> ecutwfc=30
>
> ecutrho=200
>
> occupations='fixed'
>
> nosym=.true.
>
> noinv = .true.
>
> input_dft = 'HSE'
>
> nqx1=5, nqx2=4, nqx3=1
>
> /
>
> &electrons
>
> diagonalization='david'
>
> mixing_mode = 'plain'
>
> mixing_beta = 0.7
>
> conv_thr =  1.0d-8
>
> /
>
> ATOMIC_SPECIES
>
> P  30.9738  p_pbe_v1.uspp.F.UPF
>
> K_POINTS automatic
>
> 10 8 1 0 0 0
>
> ATOMIC_POSITIONS (crystal)
>
> P   0.50  0.914274  0.002447
>
> P   0.00  0.585727  0.002447
>
> P   0.00  0.414273  0.167618
>
> P   0.50  0.085726  0.167617
>
>
> -
>
>
>
> Best,
>
>
>
> Xiaoming Wang
>
>
>
> IAMDN, Rutgers
>
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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
  !---
  SUBROUTINE exx_n_plane_waves(ecutwfc, tpiba2, g, ngm, npwx)
!---
!
! Find maximum number of plane waves npwx among the entire grid of k and
! of k+q points - should be called after a previous call to n_plane_waves 
! (for k-points only), providing in input the value of npwx found by
! n_plane_waves, to ensure that the final npwx is the largest of the two
!
USE kinds, ONLY : DP
USE funct, ONLY : dft_is_hybrid
USE uspp,  ONLY : okvan
IMPLICIT NONE
!
INTEGER, INTENT(in)  :: ngm
REAL(DP),INTENT(in)  :: ecutwfc, tpiba2, g (3, ngm)
INTEGER, INTENT(inout) :: npwx
INTEGER, ALLOCATABLE :: ngkq(:)
INTEGER :: npwx_
!
IF( .NOT. okvan .OR. .NOT.dft_is_hybrid() ) RETURN
IF( .NOT.exx_grid_initialized) &
CALL errore("exx_n_plane_waves","you must initialize the grid first",1)
ALLOCATE(ngkq(nkqs))
CALL n_plane_waves (ecutwfc, tpiba2, nkqs, xkq_collect, g, ngm, npwx_, ngkq)
DEALLOCATE(ngkq)
npwx = MAX (npwx, npwx_)
!
RETURN
!
  END SUBROUTINE exx_n_plane_waves
  !
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Re: [Pw_forum] Magnetization

[BARRETEAU Cyrille]

I find it a bit strange that you get such a small difference between magnetic 
and non magnetic solution...
Even systems extremely close to magnetism such as Pd have a larger difference.
You should give more information about your system (and input file.)

Cyrille


Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE

DTU Nanotech
Ørsteds Plads, building 345E
DK-2800 Kgs. Lyngby,  DENMARK

+33 1 69 08 29 51 /+33  6 47 53 66 52  (mobile)   (Fr)
+4545 25 63 12/ +45 28 72 55 18  (mobile)  (Dk)
email: cyrille.barret...@cea.fr  /cyr...@nanotech.dtu.dk
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/


De : pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] de la part de 
Giovanni Cantele [giovanni.cant...@spin.cnr.it]
Envoyé : vendredi 3 juillet 2015 11:58
À : PWSCF Forum
Objet : Re: [Pw_forum] Magnetization

I would say that, strictly speaking, because the lowest energy solution 
corresponds to the most stable system, your system is not magnetic. However, in 
your case it seems that the energy difference between the different solutions 
is not that large (NM-FM ~ 2 meV).

Maybe, giving more details on your system and, possibly, input files, could 
help in understanding if your results are correct. For example: does the 
magnetic solution require a supercell? Did you carefully check the convergence 
with respect to the calculation parameters? If you use supercells and k-point 
sampling, you must, especially for so small energy differences, use k-point 
grids that are equivalent as far as convergence is concerned . What about the 
convergence with respect to cutoff?

Giovanni


On 01 Jul 2015, at 16:11, fadwa fad 
mailto:fadwa.m...@gmail.com>> wrote:


Dear Giovanni
Thanks so much

I did the three different initial magnetizations corresponding to a non
magnetic, a ferromagnetic and antiferromagnetic state, I found for 
ferromagnetic that :

total magnetization = 0.76 Bohr mag/cell

absolute magnetization = 0.85 Bohr mag/cell

But when I compared the energies I found : -87.25674493 Ry for FM(highest 
energy),  -87.25674496  Ry for AFM and -87.25692574 Ry for NM (lowest energy).

so How can I interpret this results? and my system is magnetic or not?

Thanks so much

Best Regards



2015-06-30 13:42 GMT+01:00 fadwa fad 
mailto:fadwa.m...@gmail.com>>:
Hi All,

I used  system that is not magnetic and I added some dopants to render it 
magnetic. My question is How can I know that the system become magnetic or not 
with pwscf? and which type of magnetization is it ?
Any help will be highly appreciated.

Kind Regards
Fadwa



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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.na.infn.it/~cantele

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Re: [Pw_forum] Smearing Problem

[Nicola Marzari]

On 02/07/2015 20:24, paresh rout wrote:
> Hello Sir,
> The units are in mRy. I tried with halving and doubling the F-D smearing
> value and the energy difference remains same (0.06mRy/atom) using
> largest k-point sampling. Can I rely on this  F-D smearing (0.00184)
> results now ? I am also doing a convergent test on MV smearing with the
> largest k-point sampling.
>
> Kind Regards
>
> Paresh
>


yes, the results are "computationally" converged - but the difference is 
so small
that you cannot draw any conclusions on what the real physical system will
want to do.

nicola


--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
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Re: [Pw_forum] Error in routine d_matrix_so

[Rajdeep Banerjee]

Dear Prof. Paolo Giannozzi,
 ok, I'll run it in espresso-5.1.1
and get back to you.


Thanks and regards,
-- 
Rajdeep Banerjee
PhD student
JNCASR, Bangalore
India
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Re: [Pw_forum] Magnetization

[Giovanni Cantele]

I would say that, strictly speaking, because the lowest energy solution 
corresponds to the most stable system, your system is not magnetic. However, in 
your case it seems that the energy difference between the different solutions 
is not that large (NM-FM ~ 2 meV).

Maybe, giving more details on your system and, possibly, input files, could 
help in understanding if your results are correct. For example: does the 
magnetic solution require a supercell? Did you carefully check the convergence 
with respect to the calculation parameters? If you use supercells and k-point 
sampling, you must, especially for so small energy differences, use k-point 
grids that are equivalent as far as convergence is concerned . What about the 
convergence with respect to cutoff?

Giovanni


> On 01 Jul 2015, at 16:11, fadwa fad  wrote:
> 
> Dear Giovanni 
> Thanks so much
> I did the three different initial magnetizations corresponding to a non 
> magnetic, a ferromagnetic and antiferromagnetic state, I found for 
> ferromagnetic that : 
> total magnetization = 0.76 Bohr mag/cell 
> absolute magnetization = 0.85 Bohr mag/cell
> But when I compared the energies I found : -87.25674493 Ry for FM(highest 
> energy),  -87.25674496  Ry for AFM and -87.25692574 Ry for NM (lowest 
> energy). 
> so How can I interpret this results? and my system is magnetic or not?
> Thanks so much
> 
> Best Regards
>  
> 
> 2015-06-30 13:42 GMT+01:00 fadwa fad  >:
> Hi All,
> 
> I used  system that is not magnetic and I added some dopants to render it 
> magnetic. My question is How can I know that the system become magnetic or 
> not with pwscf? and which type of magnetization is it ? 
> Any help will be highly appreciated.
> 
> Kind Regards
> Fadwa 
>  
> 
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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.na.infn.it/~cantele

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Re: [Pw_forum] projwfc.x crashes when natomwfc iz zero

[Paolo Giannozzi]

As a quick-and-dirty solution, you can "borrow" atomic wavefunctions from a
different but similar pseudopotential. You need to tweak the UPF file,
setting the correct number of wavefunctions.

Paolo

On Tue, Jun 30, 2015 at 5:56 PM, Jure Varlec  wrote:

> On Tue, 30 Jun 2015 17:04:50 +0200
> Paolo Giannozzi  wrote:
> > it is (I guess but I am quite sure) for a very specific reason: there
> > are no atomic wavefunctions. These are read from pseudopotential
> > files, but not all PP files contain them. Most computations do not
> > use, or anyway do not require, them. Projection on atomic
> > wavefunctions, of course, requires at least one of them.
>
> I see. Looking at the UPF file, it does say has_wfc="F"; now I know
> what it means. So I'm off to find another program to generate
> pseudopotentials using libxc (I wish to experiment with van der Waals
> functionals). Suggestions welcome :)
>
> Thank you very much for a quick and concise explanation.
>
> Best regards
> Jure
>
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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] Restarting nscf/bands calculation

[Lorenzo Paulatto]

On Friday, July 03, 2015 12:44:17 AM Debnath Talukdar wrote:
> It takes calculation over 40 k points in 24 hours. It also creates
> around 300 GB disk space. Could anybody gives me proper suggestion that I
> can able to restart  nscf calculation and manage this large amount of disk
> space for a single calculation.

Can't you run the k-points one by one by hand?

best regards

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Re: [Pw_forum] Restarting nscf/bands calculation

[Paolo Giannozzi]

I am quite sure that both calculations='nscf' and 'bands' can be restarted,
using option restart_mode='restart', if properly stopped by setting a CPU
time limit, or manually by an appropriate "prefix".EXIT file. If you do not
need wavefunctions for further usage, disk_io='none' should prevent writing
to file. From file Doc/release-notes:

Incompatible changes in 5.1 version:
[...] Restart mechanism of pw.x changed a lot. It works ONLY if you stop
 the code cleanly with the prefix.EXIT file, or by setting
"max_seconds";
 disk_io='high' no longer needed (use it ONLY if tight with memory)
 Restarting from hard crashes is no longer supported.

Paolo

On Thu, Jul 2, 2015 at 9:14 PM, Debnath Talukdar <
debnath.taluk...@students.iiserpune.ac.in> wrote:

> Dear all,
>   I am trying to do bands calculation of 6x6 germanene monolayer
> over 100 k points along high symmetry line of hexagonal BZ. Last year I
> tried to do it using espresso-5.0.2. At that time I saw that if I give
> calculation='bands' then it can not be restarted but if I gave
> calculation='nscf' then it restarted. But for now in espresso-5.1 I am
> unable to restart though I gave calculation='nscf' instead of
> calculation='bands' for my above band structure calculation. It is very
> difficult to handle  this type of calculation if I cannot able to restart
> it. It takes calculation over 40 k points in 24 hours. It also creates
> around 300 GB disk space. Could anybody gives me proper suggestion that I
> can able to restart  nscf calculation and manage this large amount of disk
> space for a single calculation.
>
>
>
>
>
>
> Thanks in advance
> debnath
>
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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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[Pw_forum] (no subject)

[Surender Pratap]

I want to compare my results with QE results can any body share with me
input file of GNR's results of EK ,DOS and conductance curves.I shall be
highly thankful .


regards

Surender Pratap
Research Scholar
Physics Department
BITS Pilani,Pilani Campus Rajsthan-333031(INDIA)...
Mob-7891949445


*Birla Institute of Technology & Science,* Pilani

Pilani 333031, Rajasthan, India
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Re: [Pw_forum] Error in routine d_matrix_so

[Paolo Giannozzi]

On Fri, Jul 3, 2015 at 8:55 AM, Rajdeep Banerjee 
wrote:


>  Error in routine d_matrix_so (5):
>  D_S (j=1/2) for this symmetry operation is not unitary
>
I am running it on espresso-5.0.1
>

then run it on a more recent version of QE. Nobody will waste time looking
for bugs that may have already been fixed

Paolo

Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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