[QE-users] convergence problem with non-colinear Fe impurity calculation

[Christoph Wolf]

Dear all,

Is there a trick to converge a calculation with spin-orbit and non-colinear
magnetism?

No matter what the ecutwfc/rho and k-points the "estimated scf accuracy"
does not go below 1e-5 but hovers at the same magnitude whilst slightly
changing the "absolute magnetization" (totl magnetization is constant). The
system is a single Fe impurity in MgO and the Fe pseudo is the relativistic
PSLibrary 1.0.0 one.

I tried the influence of mixing_beta and mixing_mode on the convergence but
that does not seem to help. I tried different smearing types and widths
(from 0.02 to 0.0005) to no avail as well.

Any help is greatly appreciated!

Best,
Chris

-- 
Postdoctoral Researcher
Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] users Digest, Vol 136, Issue 3

[Christoph Wolf]

Dear  Jibiao ,

the input looks OK (3 types of atoms and 8 atoms in total) but your k-grid
is very coarse. For graphene I usually use a  grid of 33 33 1 0 0 0 or
finer. To see if the individual atoms are accounted for you can project the
bands onto the DOS (PDOS) using projwfc.x which will give you atom and
orbital resolved DOS!

HTH,
Chris

On Sat, Nov 3, 2018 at 8:02 PM 
wrote:

> Send users mailing list submissions to
> users@lists.quantum-espresso.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.quantum-espresso.org/mailman/listinfo/users
> or, via email, send a message with subject or body 'help' to
> users-requ...@lists.quantum-espresso.org
>
> You can reach the person managing the list at
> users-ow...@lists.quantum-espresso.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of users digest..."
>
>
> Today's Topics:
>
>1. Graphene component is missing in band structure   calculations
>   of BN-graphene bilayer (=?ISO-8859-1?B?amliaWFvbGk=?=)
>
>
> --
>
> Message: 1
> Date: Fri, 2 Nov 2018 21:02:06 +0800
> From: "=?ISO-8859-1?B?amliaWFvbGk=?=" 
> To: "=?ISO-8859-1?B?dXNlcnM=?=" 
> Subject: [QE-users] Graphene component is missing in band structure
> calculations of BN-graphene bilayer
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear QE community,
>
>
> I try to perform band structure calculations of a BN-graphene bilayer
> using the input files below. However,the calculations seem ignoring the
> graphene part and only gives the band structure of BN (bands.dat.gnu).
> Could you tell me what's wrong with my calculations?
>
>
> I look forward to receiving your answers.
>
>
> Best
>
>
> Jibiao Li
> Yangtze Normal University, Chongqing,China
>
>
>
>
> bilayer.pw.inp:
>  &CONTROL
>  calculation = 'relax' ,
> restart_mode = 'from_scratch' ,
>   outdir = './' ,
>   pseudo_dir = '/home/jibiaoli/pseudo/' ,
>   prefix = 'bilayer' ,
>  disk_io = 'high' ,
>  /
>  &SYSTEM
>ibrav = 0,
>celldm(1) = 8.16362,
>  nat = 8,
> ntyp = 3,
>  ecutwfc = 31 ,
>  ecutrho = 180 ,
>  occupations = 'smearing' ,
>  degauss = 0.05D0 ,
> smearing = 'methfessel-paxton' ,
> vdw_corr = 'grimme-d2' ,
>  /
>  &ELECTRONS
>  mixing_beta = 0.2D0 ,
>  diagonalization = 'david' ,
>  /
>  &IONS
>  /
> CELL_PARAMETERS alat
>  1.00.00.0
>  0.00.577250.0
>  0.00.04.51171
> ATOMIC_SPECIES
> C   12.00100  C.pbe-van_ak.UPF
> B   10.81000  B.pbe-n-van.UPF
> N   14.00700  N.pbe-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> N2.879765465   0.001562883   3.112022016
> B2.159469680   1.248548313   3.111925583
> N0.719662582   1.247230054   3.111926064
> B0.0   0.0   3.1128091500   0   1
> C3.603851242   1.246706724   0.01   1   0
> C2.159647441   1.246187123   0.01   1   0
> C1.443875575  -0.000685925   0.01   1   0
> C0.0   0.0   0.00   0   0
> K_POINTS automatic
>   3 6 1   0 0 0
>
>
> band.pw.inp:
>  &CONTROL
>  calculation = 'bands' ,
>   outdir = './' ,
>   pseudo_dir = '/home/jibiaoli/pseudo/' ,
>   prefix = 'bilayer' ,
>  /
>  &SYSTEM
>ibrav = 0,
>celldm(1) = 8.16362,
>  nat = 8,
> ntyp = 3,
>  ecutwfc = 31 ,
>  ecutrho = 180 ,
>  occupations = 'smearing' ,
>  degauss = 0.05D0 ,
> smearing = 'methfessel-paxton' ,
> vdw_corr = 'grimme-d2' ,
>  /
>  &ELECTRONS
>  mixing_beta = 0.2D0 ,
>  /
> CELL_PARAMETERS alat
>  1.00.00.0
>  0.00.577250.0
>  0.00.04.51171
> ATOMIC_SPECIES
> C   12.00100  C.pbe-van_ak.UPF
> B   10.81000  B.pbe-n-van.UPF
> N   14.00700  N.pbe-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> N2.879765465   0.001562883   3.112022016
> B2.159469680   1.248548313   3.111925583
> N0.719662582   1.247230054   3.111926064
> B0.0   0.0   3.1128091500   0   1
> C3.603851242   1.246706724   0.01   1   0
> C2.159647441   1.246187123   0.01   1   0
> C1

Re: [QE-users] Trouble reading Atomic Positions from CIF file

[Aziz Fall]

Dear Pietro Davide Delugas

Thank you very much for your kind reply. I tried running the input file you
sent me using xcrysden, but I get a weird error saying that the
line = CR 3A 0.4
At line 328 of file pwi2xsf.f
Fortran runtime error: Bad real number in item 1 of list input

I have tried re-writing the file just in case there were some weird hidden
characters in the file, but that does not seem to work. Any help would be
very much appreciated.

Thank You again,
Sincerely Aziz Fall.

On Wed, Oct 31, 2018 at 5:11 AM Pietro Davide Delugas 
wrote:

> Dear Aziz
>
> you can use the CIF file coordinates directly   using the crystal_sg
> format for the coordinates in atomic positions, and specify the space_group
> number in the system namelist ( please look at the input documentation ).
>
> This information is all contained in the CIF file. You were also using the
> wrong ibrav,
> if you look at the  axes angles you can see that A and B axes are
> orthogonal to C axis and they form a 120 angle between them so I guess
> should be ibrav=4 not 5.
>
> Other thing for the CIF files includes 3 coordinates even for the 3a
> positions, 2 of them are redundant and I don't know why the programs stops
> instead of ignoring them so you have to take them off the input.
>
> You can find more information about any wyckoff position in this site
>
> http://www.cryst.ehu.es/cryst/get_wp.html
>
> I attach an input file with Wyckoff position for your case, I hope it works
>
> regards - Pietro
>
>
> On 10/30/2018 09:30 PM, Aziz Fall wrote:
>
> Dear Quantum Espresso team,
>
> I am a researcher from the University of Michigan Ann Arbor. I am still
> fairly new to Quantum Espresso. I have been recently trying to run a band
> structure calculation of CrI3. The first step I took was to write the scf
> input file for CrI3 and plug in all of the cell parameters and atomic
> positions from a corresponding CIF file that I downloaded from Springer.
> But when I visualize the scf file in XCrysden it gives me the wrong atomic
> structure, even though the atomic positions I put into it are from the cif
> file. Any help in solving this problem would be greatly appreciated. I have
> attached both my scf and cif files below.
>
>
> Thank You,
> Sincerely Aziz Fall
>
>
> ___
> users mailing 
> listusers@lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> ___
> users mailing list
> users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] [EXT] Environ Bands Not Converging

[Lance Kavalsky]

Dear Professor Andreussi,


Thank you so much for your detailed response! I changed continuum interface to 
using the soft sphere approach and it appears to have resolved the scf 
convergence issue.


It was able to complete a full scf cycle on the initial structure, but before 
starting the second cycle it crashes now giving an error of:


%%%  task # 5  from 
update_environ_charges  
 : error # 1  Inconsistent integral of total charge  
%

Interestingly, setting env_static_permittivity=1.0 in environ.in and removing 
assume_isolated = 'slabz' did not reproduce this error, and the calculation was 
able to completely finish. I also noticed in the output file just before the 
crash, it has the line "extrapolated charge  131.09828, renormalised to  
131.0" and I'm wondering if this may be related. I would very much 
appreciate any additional suggestions to address this new error.

Best,

Lance Kavalsky

University of Toronto



From: users  on behalf of Andreussi, 
Oliviero 
Sent: Thursday, November 1, 2018 6:46 PM
To: Quantum Espresso users Forum
Subject: Re: [QE-users] [EXT] Environ Bands Not Converging

Hi,

Thanks for reporting the problem. I am not sure of its source, but the defaults 
of Environ should be good enough for simple systems like yours and if you 
tested different numerical parameters without success this would suggest me 
that there is a physical reason why the calculation is not converging. My main 
guess is that the problem resides with the lithium ion. Have you tested the 
calculation without lithium? Have you tried the calculation with lithium and 
without the solvent? What pseudo potential are you using for lithium (does the 
lithium ion have just one valence electron or does it also have its core 
electrons)?

If lithium has only its valence electron and loses it to the substrate, this is 
probably going to be a problem for SCCS. In SCCS the continuum boundary is 
defined on the electronic density, so it means that the continuum goes on top 
of the lithium ion. To avoid this you could either use full potential for 
lithium or use an alternative approach for the continuum interface, namely the 
soft-sphere solvation approach (Fisicaro et al. JCTC 2017). To use the latter 
you can just specify solvent_mode = ‘ionic’. In this case, you may want to 
check that the soft-sphere radius for lithium is reasonable.

Hope this helps.

Best,

Oliviero Andreussi
--
Assistant Professor
Department of Physics
University of North Texas
Email: oliviero.andreu...@unt.edu
Phone: +1-(940)-369-5316
Skype: olivieroandreussi
Web: https://sites.google.com/site/olivieroandreussi

On Nov 1, 2018, at 5:28 PM, Lance Kavalsky 
mailto:lance.kaval...@mail.utoronto.ca>> wrote:

Hello all,

I am currently trying to use Environ and am experiencing difficulty. When 
running vc-relax I am receiving the error "bands not converged". This is 
despite changing the environ_thr, tol, solvent_mode, conv_thr, diagonalization, 
and mixing_mode. I have yet to see it complete a single full scf cycle, and 
watching the estimated scf accuracy it will periodically explode hitting values 
as large as 1700 Ry before finally giving the error message.

Any additional suggestions would be very much appreciated. Both the pw.x and 
environ.in files have been pasted below. I am using QE 6.2.1 and Environ 1.0.

Thanks,
Lance Kavalsky
University of Toronto



&control
disk_io='high'
tprnfor = .TRUE.
restart_mode = 'from_scratch',
prefix = 'all',
calculation ='vc-relax',
outdir = './all',
Pseudo_dir = '~/qe_pseudo'
nstep = 100

/

&system
assume_isolated = 'slabz'
ibrav=0,
nat=33,
nbnd=120
nosym= .TRUE
ntyp=2,
ecutwfc=60,
degauss=0.02,
occupations='smearing'
smearing='mp'
vdw_corr='grimme-d2',
/

 &electrons
mixing_mode='local-TF',
mixing_beta=0.2,
electron_maxstep=200,
conv_thr = 1.D-5
/

&ions

/

&cell

/

CELL_PARAMETERS

  18.638982356   0.0   0.0
  -9.319491169  16.141832210   0.0
   0.0   0.0  43.442244346

ATOMIC_SPECIES

C 12.0107 C.pbe-n-kjpaw_psl.0.1.UPF
Li 6.94   Li.pbe-s-kjpaw_psl.0.2.1.UPF

ATOMIC_POSITIONS angstrom

Li   2.465903098   2.847312956   7.998767559
C   -0.001222067  -0.002150713   5.748168621
C   -0.006894107   1.419668805   5.748711907
C   -1.235385692   2.135486140   5.748168054
C   -1.235385692   3.559103273   5.748168054
C   -2.465827629   4.271813207   5.747820607
C   -2.465827488   5.694593503   5.747451858
C   -3.697991730   6.405978452   5.747822309
C   -3.65777   7.827928911   5.748170451
C2.465832575  -0.007964030   5.748711231
C2.465830973   1.415317747   5.733405805
C1.225702627   2.1

[QE-users] Incompatible iflag/output_format when running pp.x calculation using QE v6.1.0

[Pacome NGUIMEYA]

Hi QE users,
I am getting the following error message when running the pp.x calculation
with *iflag=3* and *output_format=7*:

%%
 Error in routine chdens (1):
 incompatible iflag/output_format
 %%
 stopping ...
--
MPI_ABORT was invoked on rank 8 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

I have been searching on internet a way to work around this but have not
found any yet.

Could you please help me in sorting this out

I am using *Quantum Espresso 6.1.0*

My pp.x is the following:
&inputpp
  prefix = '$PREFIX',
  outdir = '/mnt/lustre/users/WORK_DIR',
 filplot = '$PREFIX.rho3dgnu',
plot_num = 0,
 /
 &plot
 nfile = 1,
 filepp(1) = '$PREFIX.rho3dgnu',
 weight(1) = 1.0,
 iflag = 3,
 output_format = 7,
   fileout = '$PREFIX.rho3dgnu.dat',
  e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
  e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
  e3(1)=0.0, e3(2)=0.0, e3(3)=1.0,
  x0(1)=0.0, x0(2)=0.0, x0(3)=0.0
 /
Thank you
Pacome
*___**_*
Pacome NGUIMEYA
Ph.D. Candidate
Computational Condensed Matter Physics
University of Cape Town (UCT), South Africa
*“Be Yourself; everyone else is already taken.” Oscar Wilde*
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users