[Pw_forum] Problem in running sumpdos.x

[efi dwi indari]

Dear QE Users,

I would like to sum up my pdos results contributed by different Iodine
ions. FYI, I am using quantum espresso-5.2.0 in Ubuntu 14.04

As what I have learned from previous discussion, I typed down this command
on the terminal:

~/Downloads/espresso-5.2.0/bin/sumpdos.x
~/FAPIis.pdos.pdos_atm#2(I)_wfc#1(s) ~/FAPIis.pdos.pdos_atm#3(I)_wfc#1(s)
~/FAPIis.pdos.pdos_atm#4(I)_wfc#1(s) > FAPIis.pdos.I_1(s).txt

I also have tried to use the '-f' and '-h' in the beginning. However, I
kept getting this error notification : bash: syntax error near unexpected
token `('

Could any body please comment on this issue? I would really appreciate it.

Thank you very much in advance.

Best Regards,

Efi Dwi Indari
Research Assistant at Institut Teknologi Bandung
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Re: [Pw_forum] Graphene Phonons Not Working

[Paolo Giannozzi]

I don't know if it is suitable, but for sure it doesn't contain that
specific bug! If you have access to v.5.3, please give it a try

Paolo

On Thu, Apr 21, 2016 at 9:53 PM, Abualnaja, Faris <
f.abualnaj...@imperial.ac.uk> wrote:

> Hi Paolo,
>
>
> On the supercomputer that I'm using, there is quantum-espresso/V.5.3.0 is
> that suitable? Or would you recommend using V.5.0.3 specifically?
>
> regards,
>
> Faris
>
> --
> *From:* pw_forum-boun...@pwscf.org  on behalf
> of Paolo Giannozzi 
> *Sent:* 21 April 2016 20:12
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] Graphene Phonons Not Working
>
>
>
> On Thu, Apr 21, 2016 at 5:42 PM, Abualnaja, Faris <
> f.abualnaj...@imperial.ac.uk> wrote:
>>
>> I've been having trouble lately trying to produce graphene phonon
>> dispersion plots. I am currently using quantum-espresso/5.0.2
>> 
>>
> V.5.0.2 has a nasty bug (fixed since v.5.0.3) that was leading to wrong
> phonons in some cases. Please try a more recent version
>
> Paolo
> --
> 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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-- 
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] Graphene Phonons Not Working

[stefano de gironcoli]

Dear Abualnaja ,

   how did you chose the smearing and k-point combination ?
   your degauss (0.1 Ry =1.36 eV) looks huge to me, while your k-point 
grid looks very dense.
   mp smearing is a good choice for *real* metals (with a significant 
dos(e_F)) even if someone would favor mv smearing. I think that in the 
case of graphene with vanishing dos(e_F) the simpler gaussian broadening 
should be fine and possibly preferable.


stefano


On 21/04/2016 20:32, Abualnaja, Faris wrote:


Apologies all in the q2r and matdyn files zasr and asr should both be 
'simple' and NOT 'crystal'





*From:* pw_forum-boun...@pwscf.org  on 
behalf of Abualnaja, Faris 

*Sent:* 21 April 2016 16:42
*To:* pw_forum@pwscf.org
*Subject:* [Pw_forum] Graphene Phonons Not Working

To whom it may concern,


I've been having trouble lately trying to produce graphene phonon 
dispersion plots. I am currently using quantum-espresso/5.0.2. I ran 
an scf calculation using an LDA norm conserving pseudo potential 
(C.pz-vbc.UPF). I found an optimised lattice parameter of 4.698 (Bohr) 
using a vc-relax calculation. I then ran an scf with the optimised 
lattice parameter and ecutwfc. I then proceeded onto producing a band 
structure with the following k-points in units of 2pi/a (Gamma (0,0,0) 
- K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). The band 
structure agrees with literature, where the dirac points meet at the K 
point. I then moved on to calculating the phonon at each k (or 
q) point. I ran the scf calculation once again in a new directory, I 
ran the phonon at gamma, K, and M. the results seemed to agree 
with literature. However, when I ran the phonon dispersion 
calculation, the results go all over the place. The gamma k and m 
points are the same but the curve is not expected. Obviously, after 
running the ph.x I ran a q2r.x calculation, followed by a matdyn.x 
calculation. To be clear I checked my k-points, I checked the k-path, 
the mp grid I used was 12x12x1 when calculating the phonon 
dispersion and 48x48x1 when running an scf calculation. Also, to 
clarify I did the tutorial for Al and Si and produced correct 
plots. Below are my input files:




 SCF 
-




  prefix = 'graphene'

  pseudo_dir = '/home/fa2215/bin/upf_files'

  calculation= 'scf'

  restart_mode   = 'from_scratch'

  verbosity  = 'high'

  tprnfor= .TRUE.

  tstress= .TRUE.

  etot_conv_thr  = 1.0D-4

  forc_conv_thr  = 1.0D-3

  nstep  = 5

  wf_collect = .TRUE.

/




  ibrav= 4

  celldm(1)= 4.698

  celldm(3)= 18.616

  nat  = 2

  ntyp = 1

  nbnd = 10

  ecutwfc  = 110

  ecutrho  = 440

  occupations  = 'smearing'

  smearing = 'mp'

  degauss  = 0.1

/




  diagonalization   = 'david'

  electron_maxstep  = 1000

  conv_thr  = 1.0e-8

  mixing_beta   = 0.3

/


ATOMIC_SPECIES

  C 12.01 C.pz-vbc.UPF

ATOMIC_POSITIONS crystal

  C 0.66 0.33  0.00

  C 0.33 0.66  0.00

K_POINTS (automatic)

48 48 1  0 0 0







-- PHONON 
-

Phonon Dispersion of graphene

 

  tr2_ph=1.0d-12

  ldisp=.true.

  nq1=12 nq2=12 nq3=1

  prefix='graphene'

  amass(1)=12.01

outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2'

  fildyn='graphene.dyn'

 /







--- Q2R 




fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc'

/

Re: [Pw_forum] Graphene Phonons Not Working

[Abualnaja, Faris]

Apologies all in the q2r and matdyn files zasr and asr should both be 'simple' 
and NOT 'crystal'



From: pw_forum-boun...@pwscf.org  on behalf of 
Abualnaja, Faris 
Sent: 21 April 2016 16:42
To: pw_forum@pwscf.org
Subject: [Pw_forum] Graphene Phonons Not Working


To whom it may concern,


I've been having trouble lately trying to produce graphene phonon dispersion 
plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation 
using an LDA norm conserving pseudo potential (C.pz-vbc.UPF). I found an 
optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I 
then ran an scf with the optimised lattice parameter and ecutwfc. I then 
proceeded onto producing a band structure with the following k-points in units 
of 2pi/a (Gamma (0,0,0) - K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). 
The band structure agrees with literature, where the dirac points meet at the K 
point. I then moved on to calculating the phonon at each k (or q) point. I ran 
the scf calculation once again in a new directory, I ran the phonon at gamma, 
K, and M. the results seemed to agree with literature. However, when I ran the 
phonon dispersion calculation, the results go all over the place. The gamma k 
and m points are the same but the curve is not expected. Obviously, after 
running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. 
To be clear I checked my k-points, I checked the k-path, the mp grid I used was 
12x12x1 when calculating the phonon dispersion and 48x48x1 when running an scf 
calculation. Also, to clarify I did the tutorial for Al and Si and produced 
correct plots. Below are my input files:



 SCF 
-



  prefix = 'graphene'

  pseudo_dir = '/home/fa2215/bin/upf_files'

  calculation= 'scf'

  restart_mode   = 'from_scratch'

  verbosity  = 'high'

  tprnfor= .TRUE.

  tstress= .TRUE.

  etot_conv_thr  = 1.0D-4

  forc_conv_thr  = 1.0D-3

  nstep  = 5

  wf_collect = .TRUE.

/




  ibrav= 4

  celldm(1)= 4.698

  celldm(3)= 18.616

  nat  = 2

  ntyp = 1

  nbnd = 10

  ecutwfc  = 110

  ecutrho  = 440

  occupations  = 'smearing'

  smearing = 'mp'

  degauss  = 0.1

/




  diagonalization   = 'david'

  electron_maxstep  = 1000

  conv_thr  = 1.0e-8

  mixing_beta   = 0.3

/


ATOMIC_SPECIES

  C 12.01 C.pz-vbc.UPF

ATOMIC_POSITIONS crystal

  C 0.66  0.33  0.00

  C 0.33  0.66  0.00

K_POINTS (automatic)

48 48 1  0 0 0







-- PHONON 
-

Phonon Dispersion of graphene

 

  tr2_ph=1.0d-12

  ldisp=.true.

  nq1=12 nq2=12 nq3=1

  prefix='graphene'

  amass(1)=12.01

  
outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2'

  fildyn='graphene.dyn'

 /







--- Q2R 




fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc'

/







 MATDYN 
---



asr='crystal'

amass(1)=12.01

flfrc='graphene.fc'

 

Re: [Pw_forum] Work function issues

[Ian Shuttleworth]

Hi Steven

I've just used H and Pt.pbe-mt_fhi.UPF recently and investigated work
function (amongst other things) and I didn't encounter any problems:

Controlled FCC/on-top binding of H/Pt(111) using surface stress

http://dx.doi.org/10.1016/j.apsusc.2016.03.173


With thanks


Ian

On Thu, Apr 21, 2016 at 4:57 PM, Hepplestone, Steven <
s.p.hepplest...@exeter.ac.uk> wrote:

> Dear all,
>
>
>
> I am having difficulties with calculating the work function of various
> metals (Au and Pt in particular) using the X.pbe-mt_fhi.UPF and
> X.pbe-n-nc.UPF pseudo potentials.  Unlike in the example in WorkFct_example
> in PP I am regularly getting a positive Fermi energy and a vacuum level
> which is lower than the average level for the potential of the atoms.  Is
> this a case of poor pseudo potential choice, a bug or user error?
>
>
>
> Any advice would be appreciated,
>
>
>
> Kind regards
>
>
>
> Steven
>
>
>
>
>
> Dr. Steven Hepplestone
>
> Physics
>
> University of Exeter
>
> Stocker Road
>
> Exeter
>
> EX4 4QL
>
> Ext.: +44 (0)1392 723048
>
> Int.: 3048
>
>
>
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[Pw_forum] Work function issues

[Hepplestone, Steven]

Dear all,

I am having difficulties with calculating the work function of various metals 
(Au and Pt in particular) using the X.pbe-mt_fhi.UPF and X.pbe-n-nc.UPF pseudo 
potentials.  Unlike in the example in WorkFct_example in PP I am regularly 
getting a positive Fermi energy and a vacuum level which is lower than the 
average level for the potential of the atoms.  Is this a case of poor pseudo 
potential choice, a bug or user error?

Any advice would be appreciated,

Kind regards

Steven


Dr. Steven Hepplestone
Physics
University of Exeter
Stocker Road
Exeter
EX4 4QL
Ext.: +44 (0)1392 723048
Int.: 3048



Au_cubic_PS2.in
Description: Au_cubic_PS2.in


Au_cubic_PS2.pp
Description: Au_cubic_PS2.pp
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[Pw_forum] Graphene Phonons Not Working

[Abualnaja, Faris]

To whom it may concern,


I've been having trouble lately trying to produce graphene phonon dispersion 
plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation 
using an LDA norm conserving pseudo potential (C.pz-vbc.UPF). I found an 
optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I 
then ran an scf with the optimised lattice parameter and ecutwfc. I then 
proceeded onto producing a band structure with the following k-points in units 
of 2pi/a (Gamma (0,0,0) - K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). 
The band structure agrees with literature, where the dirac points meet at the K 
point. I then moved on to calculating the phonon at each k (or q) point. I ran 
the scf calculation once again in a new directory, I ran the phonon at gamma, 
K, and M. the results seemed to agree with literature. However, when I ran the 
phonon dispersion calculation, the results go all over the place. The gamma k 
and m points are the same but the curve is not expected. Obviously, after 
running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. 
To be clear I checked my k-points, I checked the k-path, the mp grid I used was 
12x12x1 when calculating the phonon dispersion and 48x48x1 when running an scf 
calculation. Also, to clarify I did the tutorial for Al and Si and produced 
correct plots. Below are my input files:



 SCF 
-



  prefix = 'graphene'

  pseudo_dir = '/home/fa2215/bin/upf_files'

  calculation= 'scf'

  restart_mode   = 'from_scratch'

  verbosity  = 'high'

  tprnfor= .TRUE.

  tstress= .TRUE.

  etot_conv_thr  = 1.0D-4

  forc_conv_thr  = 1.0D-3

  nstep  = 5

  wf_collect = .TRUE.

/




  ibrav= 4

  celldm(1)= 4.698

  celldm(3)= 18.616

  nat  = 2

  ntyp = 1

  nbnd = 10

  ecutwfc  = 110

  ecutrho  = 440

  occupations  = 'smearing'

  smearing = 'mp'

  degauss  = 0.1

/




  diagonalization   = 'david'

  electron_maxstep  = 1000

  conv_thr  = 1.0e-8

  mixing_beta   = 0.3

/


ATOMIC_SPECIES

  C 12.01 C.pz-vbc.UPF

ATOMIC_POSITIONS crystal

  C 0.66  0.33  0.00

  C 0.33  0.66  0.00

K_POINTS (automatic)

48 48 1  0 0 0







-- PHONON 
-

Phonon Dispersion of graphene

 

  tr2_ph=1.0d-12

  ldisp=.true.

  nq1=12 nq2=12 nq3=1

  prefix='graphene'

  amass(1)=12.01

  
outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2'

  fildyn='graphene.dyn'

 /







--- Q2R 




fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc'

/







 MATDYN 
---



asr='crystal'

amass(1)=12.01

flfrc='graphene.fc'

flfrq='graphene.freq'

/

 219

0.000.000.00   1.0

 ::::




So to recap my procedure was as follows:


scf

phonon disp

q2r

[Pw_forum] phonon output

[Sohail Ahmad]

Dear Arrigo Calzolari
I tried to calculate at Gamma point and I am getting as follows
Mode Symmetry, C_3V (3m) point group:freq (1 - 1) = 2.5  [cm-1]    A_1  
   L_1 I + Rfreq (2 - 3 ) =   10.4 [cm-1]    E L_3  
I+Rfreq (4 - 4)  =   347.1 [cm-1]  A_1    L_1  I+Rfreq (5 - 6 ) =   
349.1 [cm-1]  E L_3  I + R

I wish to determine LO and TO frequenciesI understand that A means singly 
degenerate and E doubly degenerate, I and R for Infrared and Raman active

How can i interpret in terms of Eg(LO),  Eg(TO), Eu(LO), Eu(TO), A1g, A2u 
Which version of QE should i use to get output in this format ?
Best Wishes 
- 

Dr. Sohail AhmadKing Khalid UniversityAbha, Saudi Arabia 

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Re: [Pw_forum] SG-15 Pseudopotentials local channel

[Marton]

Hi Kayahan,

I'm not familiar with the upf2casino converter but as far as I know the
local channel in the SG-15 pseudopotentials is the "smooth polynomial
continuation of the all-electron potential" and not an angular momentum
component. I think l_local = -1 in the UPF header is consistent with this.

HTH,
Marton Voros
--
Materials Science Division
Argonne National Laboratory


Dear PWSCF Users,

I am trying to convert SG-15 pseudopotentials -PP- into CASINO format (a
popular Quantum Monte Carlo -QMC- code) using upf2casino.x in Quantum
Espresso distribution under /upftools directory.

However, the converted pseudopotential seems to get negative values for the
local angular momentum channel. I think it is because “l_local" parameter
is also set to the same value in the PP_HEADER section of the .UPF file and
the conversion script assumes that it is the local channel. Right now I am
testing the converted PP assuming that l_local-l_max which means that the
maximum angular momentum orbital is actually the local channel.

Is there anybody else who has such experience with the PP? What else should
I be looking for in order to understand the conversion is right? I would
look for some physical properties normally in DFT, but doing them in QMC
takes a very long time.

Thanks a lot in advance!

Best,
Kayahan

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Re: [Pw_forum] wannier_ham.x: Wannier orthogonalization failed.

[Dmitry Korotin]

Dear Riping Wang,
Wannier orthogonalization procedure fails if there is no enough bands
of selected symmetry within the selected bands set. In your case the
13th energy band (or even 12th one) in some k-points corresponds to a
wavefunction without any Ni-p contribution (one can check this using
projwfc.x).
One should increase the energy window for wannier functions generation
or exclude from the generation procedure the Ni-p Wannie functions.
For Wannier90 code there is the disentanglement procedure that solve
this problem. There is no public available similar procedure for
wannier_ham.x code yet.

2016-04-20 16:36 GMT+05:00 Wang Riping :
> Dear Developer
>
>
>
>
> I am now going to use wannier_ham.x
>
> I make wannier function using the same pw.x results for scf and nscf
> calculation.
>
>
> It is for the NiO case shipped as the example in quantum ESPRESSO.
>
>
> When I use one the input file provided in the ESPRESSO example, it works.
>
> But when I make modification, many Wannier orthogonalization failed.
>
> The error report like this:
>
> Computing k-point1715
> Computing k-point1716
>
>  Wannier orthogonalization failed on k-point1716 with status 1
>
> Computing k-point1717
>
>  Wannier orthogonalization failed on k-point1717 with status 1
>
> Computing k-point1718
> Computing k-point1719
>
>
>
> I attached as bellow the input file for the case without error and with
> error.
>
>
>
> wannier.in1
>
>
> 
>  prefix='NiO'
>  outdir='/home/riping/tmp/'
>  nwan = 8
>  form = amulet
> /
> WANNIER_AC
>  Wannier# 1 2 9
>  atom 1
>  d 1 1.0
>  Wannier# 2 2 9
>  atom 1
>  d 2 1.0
>  Wannier# 3 2 9
>  atom 1
>  d 3 1.0
>  Wannier# 4 2 9
>  atom 1
>  d 4 1.0
>  Wannier# 5 2 9
>  atom 1
>  d 5 1.0
>  Wannier# 6 2 9
>  atom 2
>  p 1 1.0
>  Wannier# 7 2 9
>  atom 2
>  p 2 1.0
>  Wannier# 8 2 9
>  atom 2
>  p 3 1.0
> /
>
>
>
> wannier.in2
>
>
> 
>  prefix='NiO'
>  outdir='outdir'
>  nwan = 13
>  form = amulet
> /
> WANNIER_AC
>  Wannier# 1 1 13
>  atom 1
>  s 1 1.0
>  Wannier# 2 1 13
>  atom 1
>  p 1 1.0
>  Wannier# 3 1 13
>  atom 1
>  p 2 1.0
>  Wannier# 4 1 13
>  atom 1
>  p 3 1.0
>  Wannier# 5 1 13
>  atom 1
>  d 1 1.0
>  Wannier# 6 1 13
>  atom 1
>  d 2 1.0
>  Wannier# 7 1 13
>  atom 1
>  d 3 1.0
>  Wannier# 8 1 13
>  atom 1
>  d 4 1.0
>  Wannier# 9 1 13
>  atom 1
>  d 5 1.0
>  Wannier# 10 1 13
>  atom 2
>  s 1 1.0
>  Wannier# 11 1 13
>  atom 2
>  p 1 1.0
>  Wannier# 12 1 13
>  atom 2
>  p 2 1.0
>  Wannier# 13 1 13
>  atom 2
>  p 3 1.0
> /
>
>
>
> Thank you very much.
>
>
> Riping Wang
>
> 2016.4.20
>
>
>
>
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-- 
С уважением,
Дмитрий Коротин

Best regards,
Dr. Dmitry Korotin

Institute of Metal Physics
S. Kovalevskaya, 18
620990 Yekaterinburg
Russia

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Re: [Pw_forum] patch to allow compilation with MKL FFTW3

[Paolo Giannozzi]

On Thu, Apr 21, 2016 at 10:12 AM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

>
> that bug was actually already fixed in SVN, it'll be included in the next
> version, due in a couple of weeks.
>

in less than a couple of weeks, I hope!

Paolo
-- 
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] patch to allow compilation with MKL FFTW3

[Lorenzo Paulatto]

On Wednesday, 20 April 2016 19:25:15 CEST David Strubbe wrote:
> David Strubbe
> MIT

Thank you David,
that bug was actually already fixed in SVN, it'll be included in the next 
version, due in a couple of weeks.

P.S. you can use the MKL FFT replacing -D__FFTW3 with -D__DFTI, which does not 
require the fftw3 interface (i.e. it is linked as part of mkl itself).

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115, 
4 place Jussieu 75252 Paris Cédex 05

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[Pw_forum] calculating band derivative by wave functions

[Chong Wang]

Hello,


I am trying to read wave functions from pw_export.x output. To check whether I 
have done it correctly, I calculated <\psi_n|P|\psi_n>(P is momentum operator 
and is -i\hbar\partial_r) using fourier coefficients of wave functions, which 
should be proportional to band derivative. However, it turns out this is not 
the case. Now there are two possibilities:


1. Is it because I made some mistakes while reading wave functions? I think 
pw_export.x stores fourier coefficients of wave functions in 'Eigenvectors' tag 
and fourier components are stored in 'Wfc_grids'.


2. Is <\psi_n|P|\psi_n> not proportional to band derivative using 
pseudopotentials?



calculation details:


I am using norm conserving pseudopotential with PBE xc functional.



Best!


Chong Wang

Ph.D. candidate

Institute for Advanced Study, Tsinghua University, Beijing, 100084
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