Re: [QE-users] Puzzle in calculate bandstructure

[Vahid Askarpour]

I had this problem before and the solution was to choose the number of 
divisions between high-symmetry points proportional to their lengths. So if G-X 
is the longest in BZ, the number of divisions for G-X would be the largest. QE 
gurus may know why this happens but I don’t.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Aug 11, 2024, at 11:00 AM, wangzongyi via users 
 wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear all
  I am trying to calculate the band structure of Bi2Se3 in the procession below:
1.mpirun -np $SLURM_NTASKS pw.x < scf.in > scf.out
2.mpirun -np $SLURM_NTASKS pw.x < bands.in > bands.out
3.mpirun -np $SLURM_NTASKS bands.x < pp.bands.in > pp.bands.out

However, after I finished this procession, the pp.bands.out file showed me the 
following information:


 high-symmetry point:  0. 0. 0.   x coordinate   0.
 high-symmetry point:  0. 0. 0.2167   x coordinate   0.2167
 high-symmetry point:  0.-0.5774 0.1445   x coordinate   0.2167
 high-symmetry point:  0. 0. 0.   x coordinate   0.8119
 high-symmetry point: -0.5000-0.2887 0.0722   x coordinate   1.3937

It is difficult for me to understand why the x coordinate of the second point 
and the third point turned out to be same. I am wondering whether I have made 
any error in my bands.in file . The bands.in file is shown in the following 
lines. It is worth to mention that even if I change the number before !L from 
20 to 1, the second and the third coordinate are still the same.


&CONTROL
  calculation = 'bands'
  etot_conv_thr =   5.00d-05
  forc_conv_thr =   1.00d-04
  outdir = './out/'
  prefix = 'Bi2Se3'
  pseudo_dir = '../pseudo/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/
&SYSTEM
  degauss =   1.4699723600d-02
  ecutrho =   3.60d+02
  ecutwfc =   4.50d+01
  ibrav = 0
  nat = 5
  nosym = .true.
  ntyp = 2
  nbnd = 120
  occupations = 'smearing'
  smearing = 'cold'
  noncolin = .true.
  lspinorb = .true.
  starting_magnetization(1) =   0.0d0
  starting_magnetization(2) =   0.0d0
/
&ELECTRONS
  conv_thr =   1.00d-09
  electron_maxstep = 80
  mixing_beta =   4.00d-01
/
ATOMIC_SPECIES
Bi 208.9804 Bi.NC.FR.PBEsol.stringent.UPF
Se 78.96 Se.NC.FR.PBEsol.stringent.UPF
ATOMIC_POSITIONS crystal
Bi   0.399000   0.399000   0.697000
Bi   0.601000   0.601000   0.303000
Se  -0.00  -0.00   0.50
Se   0.206000   0.206000   0.118000
Se   0.794000   0.794000   0.882000
K_POINTS crystal_b
5
0.0 0.0 0. 50 !G
0.0 0.0 0.5000 20 !Z
0.5 0.5 0. 50 !F
0.0 0.0 0. 50 !G
0.5 0.0 0. 20 !L
CELL_PARAMETERS angstrom
 -2.069000  -3.583614   0.00
  2.069000  -3.583614   0.00
  0.00   2.389075   9.546667

And my pp.bands.in file is in the following lines, I wish you could look 
through it, too.

&BANDS
  outdir = './out'
  prefix = 'Bi2Se3'
  filband = 'Bi2Se3_prim.dat'
/

I don't know what problem lead to this error coordinate. Could you please help 
me?

Thank you very much!

Zongyi Wang
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Re: [QE-users] calculation stops after bfgs step without writing atom coordinates

[Vahid Askarpour]

1. You are using FD smearing of 0.01Ry. Are you expecting a metallic silicon?

2. Forces on the atoms are large. Are you sure your supercell is generated 
correctly?

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On May 31, 2024, at 4:13 AM, Daniel Rothchild via users 
 wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Also, you said you're doing a gamma-only calculation, but I don't see the line 
"gamma-point specific algorithms are used" in your output file, which suggests 
you may be manually specifying a 1x1x1 kpoint grid instead of using "K_POINTS 
gamma". The latter roughly halves CPU and memory requirements compared to the 
former (https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm1528)

Daniel Rothchild

On Thu, May 30, 2024 at 11:59 PM Kazume NISHIDATE 
mailto:nisid...@iwate-u.ac.jp>> wrote:
Dear Antonio Cammarata

Did you set an ‘artificial number’ for the number of bands (nbnd)?

In your output file, the energy of the top four bands are
-3.4287  -3.4224  -3.4224  -3.4063

While the Fermi energy is-3.2274 ev.

Then the occupation numbers at the top four bands are
 0.8144   0.8074   0.8074   0.7882

This means that the system has no conduction bands.
Wrong setting.

Do not specify the nbnd and just use the default setting.



> 2024/05/30 16:02、Antonio Cammarata via users 
> mailto:users@lists.quantum-espresso.org>>のメール:
>
> Dear all,
>
> I am using PWSCF v.7.3 compiled with GCC 13.2.0 and scalapack on 3 nodes 
> using 32 cores per node, where each node has 256 GB RAM. The system is a 
> cluster of 512 Si atoms, so only the gamma point is used. After the scf, 
> forces on atoms are written but then the calculation stops without writing 
> the new atomic positions. Please, attached you find the output in the case 
> more details are needed. Could you suggest some optimal parameters for the 
> parallelization (for the input and the command line) to avoid the memory 
> issue? I guess that this would help to solve also this issue
>
> https://www.mail-archive.com/users@lists.quantum-espresso.org/msg44394.html
>
> Thanks a lot in advance for your kind help.
>
> Antonio
>
> --
> ___
> doc. Antonio Cammarata, PhD in Physics
> Associate Professor in Applied Physics
> Advanced Materials Group
> Department of Control Engineering - KN:G-204
> Faculty of Electrical Engineering
> Czech Technical University in Prague
> Karlovo Náměstí, 13
> 121 35, Prague 2, Czech Republic
> Phone: +420 224 35 5711
> Fax:   +420 224 91 8646
> ORCID: orcid.org/-0002-5691-0682<http://orcid.org/-0002-5691-0682>
> WoS ResearcherID: A-4883-2014
> ___
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> ___
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西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishid...@gmail.com<mailto:kazume.nishid...@gmail.com>, 
nisid...@iwate-u.ac.jp<mailto:nisid...@iwate-u.ac.jp>
https://sites.google.com/site/nisidatelab/

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Re: [QE-users] ML-MoS2 fatbands: two questions/bugs

[Vahid Askarpour]

Hi Kazume,

Thank you for checking the fatbands. Either the high cutoff is the cause of the 
spikes or  QE was not built properly on our cluster. I will redo using your 
settings and if the spikes persist, the issue is likely the QE build.

Again, thank you for this test.

Cheers,
Vahid

On May 26, 2024, at 4:07 AM, Kazume NISHIDATE  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Here is my result (fatband one).
M to K points with 100 divisions.

No spikes.

> 2024/05/25 9:15、Vahid Askarpour のメール:
>
> I do not get spikes in the band structure either ( I use PBE 
> fully-relativistic PSPs from PseudoDojo). It is the fatbands in which I get 
> the spikes. My guess is there is a bug in the plotband.x code or I might be 
> missing something here.

Your cutoff energy seems me too high.
I used the following.
——
ecutwfc =  40.0,
ecutrho = 250.0,
—


I used the pseudo-potentials of:
Mo 95.95 Mo.rel-pz-spn-rrkjus_psl.0.2.UPF
S 32.065 S.rel-pz-n-rrkjus_psl.0.1.UPF

I used the setting of ‘plotband.in’ as

MoS2.bands.dat
17 26
-5 5
MoS2.bands
MoS2.bands.ps
 0.002425
 0.1  0.002425
——





西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/

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Re: [QE-users] Error while phonon calculation (ph.x)

[Vahid Askarpour]

Dear Hasan,

GaAs is a semiconductor. Hence “fixed” occupation as confirmed by Lorenzo.

Cheers,
Vahid

On May 26, 2024, at 1:12 AM, Md. Jahid Hasan Sagor  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

I have run it with "Fixed" occupations. It works. But usually Isn't it for 
insulators (fixed occupation)?

Best
Hasan

On Fri, May 24, 2024 at 5:21 PM Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:
Why not use occupations=‘fixed’?

Cheers,
Vahid

On May 24, 2024, at 5:53 PM, Md. Jahid Hasan Sagor 
mailto:md.sa...@maine.edu>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Hi Lorenzo,

Thank you for your response. But Here I am using GaAs, it's a semiconductor, 
but still I am getting the message.

Thanks

Best
Hasan

On Fri, May 24, 2024 at 4:51 PM Lorenzo Bastonero 
mailto:lbast...@uni-bremen.de>> wrote:
Hello,

Dielectric constant in metals is “infinite”. There’s no static response to a 
static electric field (you would generate an electric current).
As such, any long-range correction to the force-constants is not needed in 
metals, if that is the reason why you were trying to compute these quantities.

Best,
Lorenzo


Lorenzo Bastonero

PhD Student
U Bremen Excellence Chair,
Bremen Center for Computational Materials Science,
and MAPEX Center for Materials and Processes

University of Bremen
Faculty of Production Engineering
TAB-Building, Room 3.32
Am Fallturm 1
28359 Bremen, DE

http://www.hmi.uni-bremen.de/

Il giorno 24 mag 2024, alle ore 22:20, Md. Jahid Hasan Sagor 
mailto:md.sa...@maine.edu>> ha scritto:

Hi Dear QE Experts,

I am trying to calculate second order force constants for GaAs. I successfully 
ran pw.x, but after that when I ran ph.x, I got the following error.

ask # 0 from phq_readin : error # 1 no electric. field with metals

Input files are attached here. I have used epsil = .true. for phonon 
calculation to calculate born charge and dielectric constant.
Would you please give some solutions for this?

Best
Md Jahid Hasan
Mechanical Engg
PhD Student
University of Maine

http://ph.in/>>http://scf.in/>>___
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Re: [QE-users] ML-MoS2 fatbands: two questions/bugs

[Vahid Askarpour]

Hi Kazume,

I do not get spikes in the band structure either ( I use PBE fully-relativistic 
PSPs from PseudoDojo). It is the fatbands in which I get the spikes. My guess 
is there is a bug in the plotband.x code or I might be missing something here.

Thanks,
Vahid

On May 24, 2024, at 9:07 PM, Kazume NISHIDATE  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Dear Vahid Askarpour,

I tried to plot the band using your input files.
I attached the band figure I just calculated along the
path of M to K with 100 k points.

My plot is just a band plot and not the 'fat' one but can't reproduce
the spikes of your figure.

I used the SSSP pseudo potentials, "Mo_ONCV_PBE-1.0.oncvpsp.upf” for
Mo and "s_pbe_v1.4.uspp.F.UPF" for S. So the difference of the pseudo
potentials may cause these spikes.




> 2024/05/25 6:46、Vahid Askarpour mailto:vh261...@dal.ca>>のメール:
>>
>> Dear QE community,
>>
>> Following the PP/examples/projected_bands_example for Pt, I have plotted the 
>> fatbands of ML-MoS2 with QE-7.2 and attached here. I have used both ibrav=0 
>> and ibrav=4 with the same outcome. I have two questions:
>>
>> 1. In the attached Mo_d-bands.png, there are spikes in the plot along K-G 
>> and M-K. Does anyone know how to eliminate them without manually editing the 
>> data?
>>
>> 2. The sum of all the weights are around 1 for most k-points but for some 
>> k-points, it is even up to 1.45. Does anyone know why the weights for some 
>> k-points are so high?
>>
>> Thank you,
>> Vahid
>>
>> Vahid Askarpour
>> Department of Physics and Atmospheric Science
>> Dalhousie University
>> Halifax, NS
>> CANADA



西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishid...@gmail.com<mailto:kazume.nishid...@gmail.com>, 
nisid...@iwate-u.ac.jp<mailto:nisid...@iwate-u.ac.jp>
https://sites.google.com/site/nisidatelab/

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[QE-users] ML-MoS2 fatbands: two questions/bugs

[Vahid Askarpour]

Dear QE community,

Following the PP/examples/projected_bands_example for Pt, I have plotted the 
fatbands of ML-MoS2 with QE-7.2 and attached here. I have used both ibrav=0 and 
ibrav=4 with the same outcome. I have two questions:

1. In the attached Mo_d-bands.png, there are spikes in the plot along K-G and 
M-K. Does anyone know how to eliminate them without manually editing the data?

2. The sum of all the weights are around 1 for most k-points but for some 
k-points, it is even up to 1.45. Does anyone know why the weights for some 
k-points are so high?

Thank you,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University
Halifax, NS
CANADA

<>
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Re: [QE-users] Error while phonon calculation (ph.x)

[Vahid Askarpour]

Why not use occupations=‘fixed’?

Cheers,
Vahid

On May 24, 2024, at 5:53 PM, Md. Jahid Hasan Sagor  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Hi Lorenzo,

Thank you for your response. But Here I am using GaAs, it's a semiconductor, 
but still I am getting the message.

Thanks

Best
Hasan

On Fri, May 24, 2024 at 4:51 PM Lorenzo Bastonero 
mailto:lbast...@uni-bremen.de>> wrote:
Hello,

Dielectric constant in metals is “infinite”. There’s no static response to a 
static electric field (you would generate an electric current).
As such, any long-range correction to the force-constants is not needed in 
metals, if that is the reason why you were trying to compute these quantities.

Best,
Lorenzo


Lorenzo Bastonero

PhD Student
U Bremen Excellence Chair,
Bremen Center for Computational Materials Science,
and MAPEX Center for Materials and Processes

University of Bremen
Faculty of Production Engineering
TAB-Building, Room 3.32
Am Fallturm 1
28359 Bremen, DE

http://www.hmi.uni-bremen.de/

Il giorno 24 mag 2024, alle ore 22:20, Md. Jahid Hasan Sagor 
mailto:md.sa...@maine.edu>> ha scritto:

Hi Dear QE Experts,

I am trying to calculate second order force constants for GaAs. I successfully 
ran pw.x, but after that when I ran ph.x, I got the following error.

ask # 0 from phq_readin : error # 1 no electric. field with metals

Input files are attached here. I have used epsil = .true. for phonon 
calculation to calculate born charge and dielectric constant.
Would you please give some solutions for this?

Best
Md Jahid Hasan
Mechanical Engg
PhD Student
University of Maine

http://ph.in/>>http://scf.in/>>___
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Re: [QE-users] Quantum espresso fails to run with La any psedupotential‏

[Vahid Askarpour]

Any reason why ATOMIC POSITIONS are specified with crystal_b instead of crystal?

Cheers,
Vahid

On Apr 10, 2024, at 5:47 PM, Gal Cohen  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear QE users i try to run the scf calculation I provide below the program 
starts and then fails without outputting error list message aside mpi-abort on 
terminal.

The last lines in the output file:

 Estimated max dynamical RAM per process >   8.68 GB

 Estimated total dynamical RAM > 138.87 GB
The error message in the terminal:
Abort(15) on node 0 (rank 0 in comm 0): application called 
MPI_Abort(MPI_COMM_WORLD, 15) - process 0

  my version of qe is 7.3.1 compiled via make as per in the instructions on 
github other input files that doesn't contain La manage to run successfully, 
trying to change the cell size did not produce other outcome.
Any insight or help would be grateful.

Best regards
Gal Cohen

p.s
here is my input file
&control
   calculation = 'scf'
   restart_mode='from_scratch'
   prefix = 'LaPtBi'
   outdir = './outdir'
   pseudo_dir = '/home/muntaser/Qe_calculations/LaPtBi'
/
&system
   ibrav = 3 , a = 20.35, b = 20.35 , c = 20.35 ,
   ecutwfc = 40 ,
   ecutrho = 370 ,
   occupations = 'smearing' ,
   smearing = 'gaussian' ,
   degauss = 0.02 ,
   lspinorb=.true.,
   noncolin=.true.,
   nat = 40 ,
   ntyp = 3 ,
   nbnd = 500 ,
/
&electrons
   conv_thr = 1.0d-10 ,
   diagonalization = 'david' ,
   mixing_mode = 'plain' ,
   startingpot = 'atomic' ,
   startingwfc = 'atomic+random' ,
   mixing_beta = 0.6 ,
/
ATOMIC_SPECIES
   La 138.90547 La.rel-pbe-spfn-kjpaw_psl.1.0.0.UPF
   Pt 195.08400 Pt.rel-pbe-n-kjpaw_psl.1.0.0.UPF
   Bi 208.98040 Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal_b
   La 0.12500 0.0 0.75000
   La 0.0 0.25000 0.37500
   La 0.0 0.75000 0.12500
   La 0.37500 1.0 0.25000
   La 0.25000 0.62500 0.5
   La 0.25000 0.37500 0.0
   La 0.5 0.25000 0.62500
   La 0.62500 0.5 0.25000
   La 0.5 0.75000 0.87500
   La 0.75000 0.87500 0.5
   La 0.87500 0.5 0.75000
   La 0.75000 0.12500 0.0
   Pt 0.0 0.25000 0.87500
   Pt 0.0 0.75000 0.62500
   Pt 0.25000 0.87500 0.0
   Pt 0.12500 0.5 0.25000
   Pt 0.25000 0.12500 0.5
   Pt 0.37500 0.5 0.75000
   Pt 0.5 0.75000 0.37500
   Pt 0.5 0.25000 0.12500
   Pt 0.62500 0.0 0.75000
   Pt 0.75000 0.62500 0.0
   Pt 0.75000 0.37500 0.5
   Pt 0.87500 0.0 0.25000
   Bi 0.08400 0.91600 0.41600
   Bi 0.08400 0.08400 0.08400
   Bi 0.16600 0.66600 0.83400
   Bi 0.16600 0.33400 0.66600
   Bi 0.41600 0.91600 0.58400
   Bi 0.33400 0.66600 0.16600
   Bi 0.33400 0.33400 0.33400
   Bi 0.41600 0.08400 0.91600
   Bi 0.66600 0.83400 0.16600
   Bi 0.58400 0.58400 0.58400
   Bi 0.58400 0.41600 0.91600
   Bi 0.66600 0.16600 0.33400
   Bi 0.83400 0.83400 0.83400
   Bi 0.91600 0.58400 0.41600
   Bi 0.91600 0.41600 0.08400
   Bi 0.83400 0.16600 0.66600
K_POINTS automatic
   3 3 3 0 0 0
___
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Re: [QE-users] [Phonopy error] "Parsing "scf-001.out" failed"

[Vahid Askarpour]

Shouldn’t tprnfor be set to .true. for scf calculations to get the forces?

Cheers,
Vahid

> On Mar 2, 2024, at 4:31 PM, Paolo Giannozzi  wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> I guess you should inquire with the developers of PhonoPy, not here.
> Before doing that, note that forces are not present in *out files. This
> does not look right to me.
> 
> Paolo
> 
> On 01/03/2024 07:05, 임용식 wrote:
>> 
>> Non si ricevono spesso messaggi di posta elettronica da
>> dydtlr5...@gm.gist.ac.kr. Informazioni sul perché è importante
>> 
>> 
>> 
>> Hello all~
>> 
>> I'm trying to draw the "Phonon dispersion" of KTaO3 using Phonopy via
>> Quantum Espresso 7.2.
>> 
>> I followed the specfic process as presented
>> here(_https://phonopy.github.io/phonopy/qe.html
>> _).
>> 
>> I made the supercell 2x2x2.
>> 
>> But in creating "FORCE_SETS", the following error occurred.:
>> 
>> -
>> 
>> _
>> 
>> _ __ | |__ ___ _ __ ___ _ __ _ _
>> 
>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
>> 
>> | |_) | | | | (_) | | | | (_) || |_) | |_| |
>> 
>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
>> 
>> |_| |_| |___/
>> 
>> 2.16.3
>> 
>> Python version 3.9.13
>> 
>> Spglib version 2.0.2
>> 
>> Calculator interface: qe
>> 
>> Displacements were read from "phonopy_disp.yaml".
>> 
>> 1.
>> 
>> *
>> 
>> * Parsing "scf-001.out" failed. *
>> 
>> *
>> 
>> 2.
>> 
>> *
>> 
>> * Parsing "scf-002.out" failed. *
>> 
>> *
>> 
>> 3.
>> 
>> *
>> 
>> * Parsing "scf-003.out" failed. *
>> 
>> *
>> 
>> FORCE_SETS could not be created.
>> 
>> ---
>> 
>> Question) What is a problem??
>> 
>> I didnt' find out the reason.
>> 
>> Would you help me?
>> 
>> Thank you.
>> 
>> Sincerely
>> 
>> P.S I attach all the input file("scf*.in", "header.in", "supercell*.in")
>> & output one( "phonopy_disp.yaml", "scf*.out").
>> 
>> Yongsik Lym
>> 
>> Gwangju Institute Science & Technology.
>> 
>> 
>> ___
>> The Quantum ESPRESSO community stands by the Ukrainian
>> people and expresses its concerns about the devastating
>> effects that the Russian military offensive has on their
>> country and on the free and peaceful scientific, cultural,
>> and economic cooperation amongst peoples
>> ___
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
> 
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
> ___
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
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___
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Re: [QE-users] kpoints.x

[Vahid Askarpour]

You should remove the first, 5th and 6th columns. Then add a new column for 
weights, which is 2/64. The factor 2 accounts for spin.

The unit will be tpiba.

I would strongly suggest that you discover these for yourself and not take what 
you are told for granted. This is how:

Run a scf calculation for a 4 4 4 1 1 1 K-grid and specify nosym=.true. in that 
file. At the beginning of the output, you will get a list of the 64 k-points in 
both crystal and cartesian. The weights are also included. See if this output 
agrees with what you know so far.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University,
Halifax, NS
CANADA

On Aug 7, 2023, at 3:54 PM, Dr. Pabitra Mandal  
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Thanks to Vahid Askarpour and Anand Jha. Your reply provides me with a better 
understanding.
I have two more queries:
1. Now, to use the kpoint mesh in the scf calculation, can I remove the 5th and 
6th column and add a new column with value 1/64 (as there are 64 kpoints, equal 
wedge of 1/64 to each kpoint for normalization to unity)?
2. Will the unit be 'tpiba', i.e., cartesian coordinates? Otherwise the value 
being more than unity of some of the components of a few kpoints can not be 
explained (If I am not wrong).
Regards...

On Mon, Aug 7, 2023 at 7:21 PM Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:
I believe the kpoints.x output coordinates are cartesian not crystal. The 5th 
column shows the multiplicity of that k-point which is in the wedge. It tells 
you how many points in the full BZ are equivalent to this wedge point. So

 1  -0.125  0.125  0.125   2.00

Means that this point in the wedge has another equivalent point in the BZ and 
that is

 64  -0.875  0.875  0.875   0.00   1

The 1 in the last column means that point 64 is equivalent to point 1. Here the 
5th column is zero suggesting that this point is not in the wedge.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University,
Halifax, NS
CANADA


On Aug 7, 2023, at 10:37 AM, Dr. Pabitra Mandal 
mailto:pabitram.so...@wbnsou.ac.in>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Also, I guess there is a problem in the generated output file from kpoints.x. 
Because, there are entries whose absolute values are more than one, viz.,
-1.125, -1.375000.
I can not bi;eave the values generated by kpoints.x.
plz help.
Also, the output file I got from kpoints.x, there are two more columns except 
for coordinate points.  What is the meaning of them?
Can I copy paste the whole file for in 'scf' calculation or need to do some 
modification?
plz help. got stuck without the answers..

On Mon, Aug 7, 2023 at 6:38 PM Dr. Pabitra Mandal 
mailto:pabitram.so...@wbnsou.ac.in>> wrote:
It would be helpful if you tell me where to find the info file for kpoint.x.


On Mon, Aug 7, 2023 at 2:04 PM Omar Ashour 
mailto:ash...@berkeley.edu>> wrote:
Dr. Mandal,

I do not think you should be using anything blindly in your calculations. The 
`info` file produced by `kpoints.x` should answer your query.

Omar A. Ashour
UC Berkeley Physics

On Mon, Aug 7, 2023 at 1:10 AM Dr. Pabitra Mandal 
mailto:pabitram.so...@wbnsou.ac.in>> wrote:
Sir,
Please let me know
i. whether I can blindly use the following output of kpoints.x in the 'scf' 
calculation prior to 'epsilon.x' calculation and
ii. what do the last and last but one column mean in the following output of 
kpoints.x

64
1  -0.125  0.125  0.125   2.00
2  -0.375 -0.125  0.375   6.00
3  -0.625 -0.375  0.625   6.00
4  -0.875 -0.625  0.875   6.00
5   0.125  0.375  0.375   0.00   2
6  -0.125  0.125  0.625   6.00
7  -0.375 -0.125  0.875  12.00
8  -0.625 -0.375  1.125  12.00
9   0.375  0.625  0.625   0.00   3
   10   0.125  0.375  0.875   0.00   7
   11  -0.125  0.125  1.125   6.00
   12  -0.375 -0.125  1.375   0.00   8
   13   0.625  0.875  0.875   0.00   4
   14   0.375  0.625  1.125   0.00   8
   15   0.125  0.375  1.375   0.00   8
   16  -0.125  0.125  1.625   0.00   4
   17  -0.375  0.375 -0.125   0.00   2
   18  -0.625  0.125  0.125   0.00   6
   19  -0.875 -0.125  0.375   0.00   7
   20  -1.125 -0.375  0.625   0.00   8
   21  -0.125  0.625  0.125   0.00   6
   22  -0.375  0.375  0.375   2.00
   23  -0.625  0.125  0.625   6.00
   24  -0.875 -0.125  0.875   0.00  11
   25   0.125  0.875  0.375   0.00   7
   26  -0.125  0.625  0.625   0.00  23
   27  -0.375  0.375  0.875   0.00  23
   28  -0.625  0.125  1.125   0.00   7
   29   0.375  1.125  0.62500

Re: [QE-users] kpoints.x

[Vahid Askarpour]

I believe the kpoints.x output coordinates are cartesian not crystal. The 5th 
column shows the multiplicity of that k-point which is in the wedge. It tells 
you how many points in the full BZ are equivalent to this wedge point. So

 1  -0.125  0.125  0.125   2.00

Means that this point in the wedge has another equivalent point in the BZ and 
that is

 64  -0.875  0.875  0.875   0.00   1

The 1 in the last column means that point 64 is equivalent to point 1. Here the 
5th column is zero suggesting that this point is not in the wedge.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University,
Halifax, NS
CANADA


On Aug 7, 2023, at 10:37 AM, Dr. Pabitra Mandal  
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Also, I guess there is a problem in the generated output file from kpoints.x. 
Because, there are entries whose absolute values are more than one, viz.,
-1.125, -1.375000.
I can not bi;eave the values generated by kpoints.x.
plz help.
Also, the output file I got from kpoints.x, there are two more columns except 
for coordinate points.  What is the meaning of them?
Can I copy paste the whole file for in 'scf' calculation or need to do some 
modification?
plz help. got stuck without the answers..

On Mon, Aug 7, 2023 at 6:38 PM Dr. Pabitra Mandal 
mailto:pabitram.so...@wbnsou.ac.in>> wrote:
It would be helpful if you tell me where to find the info file for kpoint.x.


On Mon, Aug 7, 2023 at 2:04 PM Omar Ashour 
mailto:ash...@berkeley.edu>> wrote:
Dr. Mandal,

I do not think you should be using anything blindly in your calculations. The 
`info` file produced by `kpoints.x` should answer your query.

Omar A. Ashour
UC Berkeley Physics

On Mon, Aug 7, 2023 at 1:10 AM Dr. Pabitra Mandal 
mailto:pabitram.so...@wbnsou.ac.in>> wrote:
Sir,
Please let me know
i. whether I can blindly use the following output of kpoints.x in the 'scf' 
calculation prior to 'epsilon.x' calculation and
ii. what do the last and last but one column mean in the following output of 
kpoints.x

64
1  -0.125  0.125  0.125   2.00
2  -0.375 -0.125  0.375   6.00
3  -0.625 -0.375  0.625   6.00
4  -0.875 -0.625  0.875   6.00
5   0.125  0.375  0.375   0.00   2
6  -0.125  0.125  0.625   6.00
7  -0.375 -0.125  0.875  12.00
8  -0.625 -0.375  1.125  12.00
9   0.375  0.625  0.625   0.00   3
   10   0.125  0.375  0.875   0.00   7
   11  -0.125  0.125  1.125   6.00
   12  -0.375 -0.125  1.375   0.00   8
   13   0.625  0.875  0.875   0.00   4
   14   0.375  0.625  1.125   0.00   8
   15   0.125  0.375  1.375   0.00   8
   16  -0.125  0.125  1.625   0.00   4
   17  -0.375  0.375 -0.125   0.00   2
   18  -0.625  0.125  0.125   0.00   6
   19  -0.875 -0.125  0.375   0.00   7
   20  -1.125 -0.375  0.625   0.00   8
   21  -0.125  0.625  0.125   0.00   6
   22  -0.375  0.375  0.375   2.00
   23  -0.625  0.125  0.625   6.00
   24  -0.875 -0.125  0.875   0.00  11
   25   0.125  0.875  0.375   0.00   7
   26  -0.125  0.625  0.625   0.00  23
   27  -0.375  0.375  0.875   0.00  23
   28  -0.625  0.125  1.125   0.00   7
   29   0.375  1.125  0.625   0.00   8
   30   0.125  0.875  0.875   0.00  11
   31  -0.125  0.625  1.125   0.00   7
   32  -0.375  0.375  1.375   0.00   3
   33  -0.625  0.625 -0.375   0.00   3
   34  -0.875  0.375 -0.125   0.00   7
   35  -1.125  0.125  0.125   0.00  11
   36  -1.375 -0.125  0.375   0.00   8
   37  -0.375  0.875 -0.125   0.00   7
   38  -0.625  0.625  0.125   0.00  23
   39  -0.875  0.375  0.375   0.00  23
   40  -1.125  0.125  0.625   0.00   7
   41  -0.125  1.125  0.125   0.00  11
   42  -0.375  0.875  0.375   0.00  23
   43  -0.625  0.625  0.625   0.00  22
   44  -0.875  0.375  0.875   0.00   6
   45   0.125  1.375  0.375   0.00   8
   46  -0.125  1.125  0.625   0.00   7
   47  -0.375  0.875  0.875   0.00   6
   48  -0.625  0.625  1.125   0.00   2
   49  -0.875  0.875 -0.625   0.00   4
   50  -1.125  0.625 -0.375   0.00   8
   51  -1.375  0.375 -0.125   0.00   8
   52  -1.625  0.125  0.125   0.00   4
   53  -0.625  1.125 -0.375   0.00   8
   54  -0.875  0.875 -0.125   0.00  11
   55  -1.125  0.625  0.125   0.00   7
   56  -1.375  0.375  0.375   0.00   3
   57  -0.375  1.375 -0.125   0.00   8
   58  -

Re: [QE-users] Negative frequencies for phonon dispersion in Bilayer MoS2

[Vahid Askarpour]

A few points about your inputs:

1. You may want to lower both force and energy convergence thresholds by a 
factor of 10

2. You are using smearing. Is this a metal? If not, try a fixed occupation

3. For a bilayer, the KPOINTS should be like 4 4 1 or 6 6 1. From experience, 
since your a=3 angstrom, I would start by a K-grid of 1010 1.

4. For phonon calculations, nq3=1. Your nq1 and nq2 are too small. So when 
interpolating for phonon dispersion calculations, you do not have enough 
q-points in the BZ to get a nice dispersion.

5. You may like to lower the tr2_ph to 1.0d-16. I have even gone to 1.0d-22 to 
avoid some negative frequencies.

6. Last but not least, the PSP may be the issue.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On Aug 4, 2023, at 8:00 AM, Vahid Askarpour  wrote:

If the coordinates of the atoms are correct for the bilayer, you just need to 
add vacuum by adding 15 to 20 Ang to the c value.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On Aug 4, 2023, at 7:08 AM, Giuseppe Scala  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
The c parameter is set in that way in order to have 10 angstrom vacuum between 
two sets of Bilayer in my structure. If I reduce the c parameter i think that 
my system won't be a Bilayer anymore. Is that line of reasoning wrong?

Il ven 4 ago 2023, 05:15 ANAND JHA 
mailto:anandk...@iitk.ac.in>> ha scritto:
C parameter and a parameter are wrong they are too high and low

On Thu, 3 Aug 2023 at 20:01, Giuseppe Scala 
mailto:g.sca...@campus.unimib.it>> wrote:
Hi ANAND,

Would you mind if I ask you to tell me where's the problem in the structure? 
Maybe that c parameter is too high or low?
Il gio 3 ago 2023, 12:58 ANAND JHA 
mailto:anandk...@iitk.ac.in>> ha scritto:
There is some issue in your bilayer
Try to make a new bilayer with CRYSTAL SOFTWARE

On Thu, 3 Aug 2023 at 03:55, Giuseppe Scala 
mailto:g.sca...@campus.unimib.it>> wrote:
I get negative frequencies at gamma points for Bilayer MoS2. I relaxed my 
structure and checked convergence with respect to energy cutoff. That's my 
input file for the scf calculation:

##

&CONTROL
calculation ='scf'
prefix = 'MoS2_BI'
pseudo_dir = '/home/Giuseppe'
outdir = './'
tstress = .true.
tprnfor = .true.
forc_conv_thr = 1.0d-3
nstep = 200
/

 &SYSTEM
ibrav = 4
a = 3.14296359603
c = 20.006663
nat = 6
ntyp = 2
ecutwfc = 60
ecutrho = 240
occupations = 'smearing'
degauss = 0.01
/

&ELECTRONS
mixing_beta = 0.7
conv_thr = 1.0d-8
diagonalization = 'david'
electron_maxstep=200
/

&IONS
trust_radius_max = 0.2
/
&CELL
cell_dynamics = "bfgs"
cell_dofree = '2Dxy'
/

ATOMIC_SPECIES
Mo 95.9400 Mo.pbesol-spn-kjpaw_psl.1.0.0.UPF
S 32.0660 S.pbesol-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Mo 1.5714815237 0.9072955423 6.6890512735
Mo 0.00 1.8145901001 13.377562735
 S 1.5714815237 0.9072955423 11.825385701
 S 1.5714815237 0.9072955423 14.928508325
 S 0.00 1.8145901001 8.2412092563
 S 0.00 1.8145901001 5.1381015776

K_POINTS {automatic}
4 4 4 0 0 0

#


And here my input file for ph.x


###

&inputph
prefix = 'MoS2_BI'
fildvscf = 'dvscf'
ldisp = .true.
fildyn = 'MoS2_BI.dyn'
alpha_mix(1) = 0.3
nq1 = 2,
nq2 = 2,
nq3 = 2,
tr2_ph = 1.0d-12
/


Is my bilayer wrong? I've come the exact same calculations for Bulk and 
Monolayer MoS2 and everything went smoothly

___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX 
(www.max-centre.eu<http://www.max-centre.eu/>)
users mailing list 
users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>
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___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX 
(www.max-centre.eu<http://www.max-centre.eu/>)
users mailing list 
users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
___
The Quantum ESPRESSO community stands

Re: [QE-users] Negative frequencies for phonon dispersion in Bilayer MoS2

[Vahid Askarpour]

If the coordinates of the atoms are correct for the bilayer, you just need to 
add vacuum by adding 15 to 20 Ang to the c value.

Cheers,
Vahid

Vahid Askarpour
Department of Physics
Dalhousie University
Halifax, NS
CANADA

On Aug 4, 2023, at 7:08 AM, Giuseppe Scala  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
The c parameter is set in that way in order to have 10 angstrom vacuum between 
two sets of Bilayer in my structure. If I reduce the c parameter i think that 
my system won't be a Bilayer anymore. Is that line of reasoning wrong?

Il ven 4 ago 2023, 05:15 ANAND JHA 
mailto:anandk...@iitk.ac.in>> ha scritto:
C parameter and a parameter are wrong they are too high and low

On Thu, 3 Aug 2023 at 20:01, Giuseppe Scala 
mailto:g.sca...@campus.unimib.it>> wrote:
Hi ANAND,

Would you mind if I ask you to tell me where's the problem in the structure? 
Maybe that c parameter is too high or low?
Il gio 3 ago 2023, 12:58 ANAND JHA 
mailto:anandk...@iitk.ac.in>> ha scritto:
There is some issue in your bilayer
Try to make a new bilayer with CRYSTAL SOFTWARE

On Thu, 3 Aug 2023 at 03:55, Giuseppe Scala 
mailto:g.sca...@campus.unimib.it>> wrote:
I get negative frequencies at gamma points for Bilayer MoS2. I relaxed my 
structure and checked convergence with respect to energy cutoff. That's my 
input file for the scf calculation:

##

&CONTROL
calculation ='scf'
prefix = 'MoS2_BI'
pseudo_dir = '/home/Giuseppe'
outdir = './'
tstress = .true.
tprnfor = .true.
forc_conv_thr = 1.0d-3
nstep = 200
/

 &SYSTEM
ibrav = 4
a = 3.14296359603
c = 20.006663
nat = 6
ntyp = 2
ecutwfc = 60
ecutrho = 240
occupations = 'smearing'
degauss = 0.01
/

&ELECTRONS
mixing_beta = 0.7
conv_thr = 1.0d-8
diagonalization = 'david'
electron_maxstep=200
/

&IONS
trust_radius_max = 0.2
/
&CELL
cell_dynamics = "bfgs"
cell_dofree = '2Dxy'
/

ATOMIC_SPECIES
Mo 95.9400 Mo.pbesol-spn-kjpaw_psl.1.0.0.UPF
S 32.0660 S.pbesol-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Mo 1.5714815237 0.9072955423 6.6890512735
Mo 0.00 1.8145901001 13.377562735
 S 1.5714815237 0.9072955423 11.825385701
 S 1.5714815237 0.9072955423 14.928508325
 S 0.00 1.8145901001 8.2412092563
 S 0.00 1.8145901001 5.1381015776

K_POINTS {automatic}
4 4 4 0 0 0

#


And here my input file for ph.x


###

&inputph
prefix = 'MoS2_BI'
fildvscf = 'dvscf'
ldisp = .true.
fildyn = 'MoS2_BI.dyn'
alpha_mix(1) = 0.3
nq1 = 2,
nq2 = 2,
nq3 = 2,
tr2_ph = 1.0d-12
/


Is my bilayer wrong? I've come the exact same calculations for Bulk and 
Monolayer MoS2 and everything went smoothly

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[QE-users] Procedure for relaxation of antiferromagnetic Mn3Ir

[Vahid Askarpour]

Dear QE Community,

Does anyone know the procedure for relaxing an antiferromagnetic structure such 
as Mn3Ir? There are some online materials but are mostly scf calculations and 
not relaxation. Any suggestions is appreciated.

Thanks,
Vahid

Vahid Askarpour
Department of Physics,
Dalhousie University
Halifax, NS
CANADA
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Re: [QE-users] Orthorhombic unit cell

[Vahid Askarpour]

Usually, if there is x-ray data on single crystals, the wyckoff positions are 
given there. Alternatively, one can use evolutionary algorithms such as USPEX 
to generate stable structures but this could be time consuming.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, Canada

On Mar 9, 2023, at 1:03 PM, sally issa  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Good morning all,

Is there anyone have worked with orthorhombic cell?
I want to define the unit cell for orthorhombic with 4 atoms:(0,y,1/4),(0,-y, 
3/4), (1/2, y+1/2, 1/4) and (-1/2, -y+1/2, 3/4).
With wyckoff position (4c).
I don’t have idea how define y.
Do you have suggestions ?

Thank you
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[QE-users] Wrong r2r4 value for Ba in the dft-d3 code

[Vahid Askarpour]

Dear QE Community,

In the file core.f90 of the dft-d3 folder of QE-7.0, the r2r4 data for Ba is 
given as 0.15679528_wp (column 1 line 12 of the data r2r4 Table).

&0.15679528_wp, 9.35167836_wp, 9.06926079_wp, 8.97241155_wp, 8.90092807_wp,&

The correct value is 10.15679528_wp. The correct value is confirmed through the 
Abinit code and the D3 code from Grimme’s website.

The change is a factor of 100 which makes C8 off by 10,000. In our case, the D3 
dispersion energy changed by a factor of 3 because of this error.

Regards,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
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Re: [QE-users] Missing subroutine in QE-7.0/dft-d3 folder

[Vahid Askarpour]

Thanks Paolo. I should have made my search case sensitive.

Best,
Vahid

On Jun 20, 2022, at 9:26 AM, Paolo Giannozzi 
mailto:paolo.gianno...@uniud.it>> wrote:

grep -i set_criteria *f90

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[QE-users] Missing subroutine in QE-7.0/dft-d3 folder

[Vahid Askarpour]

Dear QE Community,

In the dft-d3 folder, there are multiple calls to a subroutine called 
“set_criteria”. I cannot find this subroutine in the QE package. Does anyone 
know where it is located?

Interestingly, in the following link 
(https://github.com/dftbplus/dftd3-lib/blob/main/lib/core.f90), this subroutine 
exists as follows:


 subroutine SET_CRITERIA(rthr,lat,tau_max)
real(wp), intent(in) :: rthr
real(wp), intent(in) :: lat(3,3)
real(wp), intent(out) :: tau_max(3)
real(wp) :: r_cutoff
real(wp) :: norm1(3),norm2(3),norm3(3)
real(wp) :: cos10,cos21,cos32

r_cutoff=sqrt(rthr)
! write(*,*) 'lat',lat
call kreuzprodukt(lat(:,2),lat(:,3),norm1)
call kreuzprodukt(lat(:,3),lat(:,1),norm2)
call kreuzprodukt(lat(:,1),lat(:,2),norm3)
! write(*,*) 'norm2',norm2
norm1=norm1/VECTORSIZE(norm1)
norm2=norm2/VECTORSIZE(norm2)
norm3=norm3/VECTORSIZE(norm3)
! write(*,*) 'norm2_',norm2
cos10=SUM(norm1*lat(:,1))
cos21=SUM(norm2*lat(:,2))
cos32=SUM(norm3*lat(:,3))
tau_max(1)=abs(r_cutoff/cos10)
tau_max(2)=abs(r_cutoff/cos21)
tau_max(3)=abs(r_cutoff/cos32)
! write(*,'(3f8.4)')tau_max(1),tau_max(2),tau_max(3)
  end subroutine SET_CRITERIA


Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

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[QE-users] A question regarding s8 in the dft-d3 code

[Vahid Askarpour]

Dear QE Community,

In the core.f90 of dft-d3  folder of QE-7.0, when calculating the BJ damping 
with version 4, the energies are given by

e6=e6+ c6/(r6+(a1*tmp+a2)**6)
e8=e8+ c8/(r8+(a1*tmp+a2)**8)

These expressions are similar to the Eqs. 5 and 6 in Journal of Computational 
Chemistry (https://doi.org/10.1002/jcc.21759) by Grimme et al. except that the 
s6 and s8 (s18 in the code) are missing. Actually s6 is set to 1.0 for version 
4 but what about s8? Shouldn’t c8 change to s8*c8 in the above second equation?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
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Re: [QE-users] Error - unknown cell_dofree ibrav

[Vahid Askarpour]

Congratulations for passing Paolo’s test of the functionality of the mailing 
list.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Apr 28, 2022, at 6:50 AM, remya ud 
mailto:remyau...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear all,
Finally, the 'unknown cell_dofree 'ibrav ' error that occurred during VC 
relaxation calculation is solved. Initially, I installed pw.x of the old 
version. Recently, Q.E.7.0 is installed. But the program was running on the 
previous version.
Sorry for the inconvenience.
thank you

On Thu, Apr 28, 2022 at 10:46 AM remya ud 
mailto:remyau...@gmail.com>> wrote:
Dear all,
I am trying to do the vc_relax calculation of Si. But it cracked with an error
task # 0
 from  init_dofree: error # 1
  unknown cell_dofree ibrav

I am using the 7.0 version of the Quantum espresso. And also checked in 
Modules/cell_base.f90 as suggested by the mailing list. When I tried with 
'all', 'shape', and 'volume', they didn't show similar errors. Kindly correct 
me where I went wrong in the calculation since 'ibrav' is working for others.

Input file is
&CONTROL
calculation ='vc-relax'
prefix = 'si'
outdir = './ outdir'
pseudo_dir = '.'
etot_conv_thr = 1e-5
forc_conv_thr = 1e-4
 /

 &SYSTEM
ibrav = 2
celldm(1) = 14
nat = 2
ntyp = 1
ecutwfc = 30
 /

 &ELECTRONS
   conv_thr=1.e-7
 /
&ions
/
&cell
   cell_dofree='ibrav'
/
ATOMIC_SPECIES
 Si  28.0855  Si.pbe-n-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS alat
 Si 0.00 0.00 0.00 0 0 0
 Si 0.25 0.25 0.25 0 0 0

K_POINTS automatic
  4 4 4 0 0 0


The  subroutine start with
SUBROUTINE init_dofree ( cell_dofree )
 !! Set constraints on cell dynamics/optimization

 CHARACTER(LEN=*), INTENT(IN) :: cell_dofree
 CHARACTER(LEN=80) :: cell_dofree_

 IF(cell_dofree(1:5) == 'ibrav') THEN
   iforceh = 1
   enforce_ibrav = .true.
   IF(cell_dofree(6:6)=="+")THEN
 cell_dofree_ = cell_dofree(7:)
   ELSE
 cell_dofree_="default"
   ENDIF
 ELSE
   cell_dofree_ = cell_dofree
 ENDIF

 SELECT CASE ( TRIM( cell_dofree_ ) )

CASE ( 'all', 'default', '' )
  iforceh = 1
!CASE ('ibrav')
  !iforceh = 1
  !enforce_ibrav = .true.
CASE ( 'shape' )
  iforceh = 1
  fix_volume = .true.
Kindly suggest some solution to solve this.



--
Remya. U. D
Research Scholar
Intermetallics and Nonlinear Optical Lab
National Institute of Technology
Tiruchirappalli, Tamil Nadu
India




--
Remya. U. D
Research Scholar
Intermetallics and Nonlinear Optical Lab
National Institute of Technology
Tiruchirappalli, Tamil Nadu
India
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Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Vahid Askarpour]

Dear Iurii,

Thank you for the clarification and the reference. It seems that I have much to 
learn.

Cheers,
Vahid

On Feb 3, 2022, at 10:13 AM, Iurii TIMROV 
mailto:iurii.tim...@epfl.ch>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

> I am getting large U parameters (~60 and 20eV) for the two species and am 
> trying to figure out if these values are realistic or not.

They are not!

For closed-shell systems the U value is unphysically large: K. Yu and E.A. 
Carter, J. Chem. Phys. 140, 121105 (2014).
This is a well-known limitation of the current method to determine U.

HTH

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
____
From: Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Thursday, February 3, 2022 2:57:07 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

Hi Iurii and Iman,

I tried  your second test (the first test failed) using find_atpert=1 and 
docc_thr=1.D-15 in my input and the hp.x code perturbed all atoms and the 
reconstruction error was avoided. I am getting large U parameters (~60 and 
20eV) for the two species and am trying to figure out if these values are 
realistic or not. The new bandgap is ~ 9eV but I was expecting around 3-4eV. 
The U=0 gap is ~2eV.

Cheers,
Vahid

On Feb 3, 2022, at 9:13 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Iman Bezzaoui,

Please remember to sign your posts.

We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Bezzaoui Iman 
mailto:imanbezza...@gmail.com>>
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
RépondreTransférer
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Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Vahid Askarpour]

Hi Iurii and Iman,

I tried  your second test (the first test failed) using find_atpert=1 and 
docc_thr=1.D-15 in my input and the hp.x code perturbed all atoms and the 
reconstruction error was avoided. I am getting large U parameters (~60 and 
20eV) for the two species and am trying to figure out if these values are 
realistic or not. The new bandgap is ~ 9eV but I was expecting around 3-4eV. 
The U=0 gap is ~2eV.

Cheers,
Vahid

On Feb 3, 2022, at 9:13 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Iman Bezzaoui,

Please remember to sign your posts.

We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Bezzaoui Iman 
mailto:imanbezza...@gmail.com>>
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
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Re: [QE-users] possible bug in bands calculation

[Vahid Askarpour]

The problem is related to different segments in the BZ not being the same 
length but all are divided into 50 points according to your input. The issue 
can be resolved if you divide the segments  according to almost their lengths. 
So if G-M is twice longer than M-L, then divide the first by 50 and the second 
by 25.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Jan 24, 2022, at 1:25 PM, Aleksandra Oranskaia 
mailto:aleksandra.oransk...@kaust.edu.sa>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Hi!

I see some weirdness that would highly appreciate help with or comments.

This is bands pathway for ibrav = 7:
K_POINTS crystal_b
8
0.0 0.0 0.0 50 !G
0.5 0.0 0.0 50 !M
0.5 0.0 0.5 50 !L
0.0 0.0 0.0 50 !G
0.5 0.5 0.0 50 !K
0.5 0.5 0.5 50 !H
0.0 0.0 0.0 50 !G
0.0 0.0 0.5 1  !A

>From bands.x output:
 Reading collected, re-writing distributed wavefunctions
 high-symmetry point:  0. 0. 0.   x coordinate   0.
 high-symmetry point:  0.5000 0.2887 0.   x coordinate   0.5774
 high-symmetry point:  0.5000 0.2887 0.1648   x coordinate   0.7421
 high-symmetry point:  0. 0. 0.   x coordinate   1.3425
 high-symmetry point:  0.5000 0.8660 0.   x coordinate   2.3425
 high-symmetry point:  0.5000 0.8660 0.1648   x coordinate   2.5073
 high-symmetry point:  0. 0. 0.   x coordinate   2.5073
 high-symmetry point:  0. 0. 0.1648   x coordinate   2.6720

I am not sure prelast point should be like this and not 3.2508, 3.6856.

This result was obtained by 6.4 and 6.8 versions.

--
Best wishes,
Alex (she/her/hers),
phd candidate in chemical sciences
'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
https://cpms.kaust.edu.sa/


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Re: [QE-users] Reconstruction problem in hp.x

[Vahid Askarpour]

Dear Iurii,

I rerun the hp.x using q-e-qe-7.0. I could avoid the same crash if I use a 
dist_thr=7.0 in the hp.in which seems to me quite large. Also some of the U 
parameters come out negative and some are "**” which I guess they are 
too large for the format.

I will keep digging into the code to see if I can find the source of this crash.

Cheers,
Vahid

On Jan 12, 2022, at 8:31 AM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear Iurii,

Thank you for taking the time to look at my files. Yes, I did recompile hp.x 
first and then pw.x for QE-6.5. I did not realize that the dist_thr existed. 
The documentation online for QE is version 7.0 for QE and 6.6 for hp.x.

I will try the latest version of the code with dist_thr and that will hopefully 
resolve the issue.

I very much appreciate your suggestion.

Cheers,
Vahid

On Jan 12, 2022, at 8:20 AM, Iurii TIMROV 
mailto:iurii.tim...@epfl.ch>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Dear Vahid,

You are using QE6.5. This is quite old. I recommend to use the latest version 
QE7.0 because it has different bug fixes.

I am surprised that increasing eps_dist does not solve the problem. Are you 
sure you do it properly? Did you recompile pw.x and hp.x after making this 
change? Note that in QE7.0 you do not need to do that because there is a new 
input parameter for hp.x which  is called dist_thr which replaces eps_dist. So 
in QE7.0 there is no need to recompile the pw.x and hp.x codes, instead just 
set dist_thr in the hp.x input and change its values from the default 6.d-4 
(Bohr) to some larger value.

HTH

Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
____
From: Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Tuesday, January 11, 2022 6:33:03 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Reconstruction problem in hp.x

Dear Iurii,

I asked permission from my supervisor if I could share the input files. He 
suggested that I share it with only you and not all the users in the Forum. Is 
it possible to send the files to you only?

Thanks,
Vahid

On Jan 11, 2022, at 4:47 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

Could you share all your input and output files via Google Drive? I will have a 
closer look at this problem.

Greetings,
Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Tuesday, January 11, 2022 3:17:19 AM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Reconstruction problem in hp.x

Dear QE Community,

I am running Hubbard U on a relaxed slab of 96 atoms with a 25Angstrom vacuum. 
I generated all the response function matrices (using sum_pertq) but when using 
compute_hp to collect all the chi0 and chi matrices, I get the following error:

   Many lines similar to the ones below

Missing chi element for: na=   288  nb=89  dist=  21.669460


 Missing chi element for: na=   288  nb=91  dist=  19.080347


 Missing chi element for: na=   288  nb=   161  dist=   7.914550


 Missing chi element for: na=   288  nb=   163  dist=  18.450123


 Missing chi element for: na=   288  nb=   233  dist=  12.788988


 Missing chi element for: na=   288  nb=   235  dist=   7.619240

Possible solutions:
 1. Relax better the structure (in order to have more accurate inter-atomic 
distances)
 2. Increase the value of the parameter eps_dist in PW/src/ldaU.f90,
then recompile the pw.x and hp.x codes, and re-run the HP 
postprocessing step
by setting compute_hp=.true. in the HP input.

 %%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
 %%

The structure is relaxed and the forces are quite small with zero stress on the 
cell.

I increased eps_dist to 0.1 and still get the above error.

Any suggestion as to how to avoid this error is deeply appreciated.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
___
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Re: [QE-users] Reconstruction problem in hp.x

[Vahid Askarpour]

Dear Iurii,

Thank you for taking the time to look at my files. Yes, I did recompile hp.x 
first and then pw.x for QE-6.5. I did not realize that the dist_thr existed. 
The documentation online for QE is version 7.0 for QE and 6.6 for hp.x.

I will try the latest version of the code with dist_thr and that will hopefully 
resolve the issue.

I very much appreciate your suggestion.

Cheers,
Vahid

On Jan 12, 2022, at 8:20 AM, Iurii TIMROV 
mailto:iurii.tim...@epfl.ch>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Dear Vahid,

You are using QE6.5. This is quite old. I recommend to use the latest version 
QE7.0 because it has different bug fixes.

I am surprised that increasing eps_dist does not solve the problem. Are you 
sure you do it properly? Did you recompile pw.x and hp.x after making this 
change? Note that in QE7.0 you do not need to do that because there is a new 
input parameter for hp.x which  is called dist_thr which replaces eps_dist. So 
in QE7.0 there is no need to recompile the pw.x and hp.x codes, instead just 
set dist_thr in the hp.x input and change its values from the default 6.d-4 
(Bohr) to some larger value.

HTH

Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Tuesday, January 11, 2022 6:33:03 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Reconstruction problem in hp.x

Dear Iurii,

I asked permission from my supervisor if I could share the input files. He 
suggested that I share it with only you and not all the users in the Forum. Is 
it possible to send the files to you only?

Thanks,
Vahid

On Jan 11, 2022, at 4:47 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

Could you share all your input and output files via Google Drive? I will have a 
closer look at this problem.

Greetings,
Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Tuesday, January 11, 2022 3:17:19 AM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Reconstruction problem in hp.x

Dear QE Community,

I am running Hubbard U on a relaxed slab of 96 atoms with a 25Angstrom vacuum. 
I generated all the response function matrices (using sum_pertq) but when using 
compute_hp to collect all the chi0 and chi matrices, I get the following error:

   Many lines similar to the ones below

Missing chi element for: na=   288  nb=89  dist=  21.669460


 Missing chi element for: na=   288  nb=91  dist=  19.080347


 Missing chi element for: na=   288  nb=   161  dist=   7.914550


 Missing chi element for: na=   288  nb=   163  dist=  18.450123


 Missing chi element for: na=   288  nb=   233  dist=  12.788988


 Missing chi element for: na=   288  nb=   235  dist=   7.619240

Possible solutions:
 1. Relax better the structure (in order to have more accurate inter-atomic 
distances)
 2. Increase the value of the parameter eps_dist in PW/src/ldaU.f90,
then recompile the pw.x and hp.x codes, and re-run the HP 
postprocessing step
by setting compute_hp=.true. in the HP input.

 %%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
 %%

The structure is relaxed and the forces are quite small with zero stress on the 
cell.

I increased eps_dist to 0.1 and still get the above error.

Any suggestion as to how to avoid this error is deeply appreciated.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
___
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Q

Re: [QE-users] Reconstruction problem in hp.x

[Vahid Askarpour]

Dear Iurii,

I asked permission from my supervisor if I could share the input files. He 
suggested that I share it with only you and not all the users in the Forum. Is 
it possible to send the files to you only?

Thanks,
Vahid

On Jan 11, 2022, at 4:47 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

Could you share all your input and output files via Google Drive? I will have a 
closer look at this problem.

Greetings,
Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Tuesday, January 11, 2022 3:17:19 AM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Reconstruction problem in hp.x

Dear QE Community,

I am running Hubbard U on a relaxed slab of 96 atoms with a 25Angstrom vacuum. 
I generated all the response function matrices (using sum_pertq) but when using 
compute_hp to collect all the chi0 and chi matrices, I get the following error:

   Many lines similar to the ones below

Missing chi element for: na=   288  nb=89  dist=  21.669460


 Missing chi element for: na=   288  nb=91  dist=  19.080347


 Missing chi element for: na=   288  nb=   161  dist=   7.914550


 Missing chi element for: na=   288  nb=   163  dist=  18.450123


 Missing chi element for: na=   288  nb=   233  dist=  12.788988


 Missing chi element for: na=   288  nb=   235  dist=   7.619240

Possible solutions:
 1. Relax better the structure (in order to have more accurate inter-atomic 
distances)
 2. Increase the value of the parameter eps_dist in PW/src/ldaU.f90,
then recompile the pw.x and hp.x codes, and re-run the HP 
postprocessing step
by setting compute_hp=.true. in the HP input.

 %%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
 %%

The structure is relaxed and the forces are quite small with zero stress on the 
cell.

I increased eps_dist to 0.1 and still get the above error.

Any suggestion as to how to avoid this error is deeply appreciated.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
___
Quantum ESPRESSO is supported by MaX 
(www.max-centre.eu<http://www.max-centre.eu/>)
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users mailing list users@lists.quantum-espresso.org
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[QE-users] Reconstruction problem in hp.x

[Vahid Askarpour]

Dear QE Community,

I am running Hubbard U on a relaxed slab of 96 atoms with a 25Angstrom vacuum. 
I generated all the response function matrices (using sum_pertq) but when using 
compute_hp to collect all the chi0 and chi matrices, I get the following error:

   Many lines similar to the ones below

Missing chi element for: na=   288  nb=89  dist=  21.669460


 Missing chi element for: na=   288  nb=91  dist=  19.080347


 Missing chi element for: na=   288  nb=   161  dist=   7.914550


 Missing chi element for: na=   288  nb=   163  dist=  18.450123


 Missing chi element for: na=   288  nb=   233  dist=  12.788988


 Missing chi element for: na=   288  nb=   235  dist=   7.619240

Possible solutions:
 1. Relax better the structure (in order to have more accurate inter-atomic 
distances)
 2. Increase the value of the parameter eps_dist in PW/src/ldaU.f90,
then recompile the pw.x and hp.x codes, and re-run the HP 
postprocessing step
by setting compute_hp=.true. in the HP input.

 %%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
 %%

The structure is relaxed and the forces are quite small with zero stress on the 
cell.

I increased eps_dist to 0.1 and still get the above error. 

Any suggestion as to how to avoid this error is deeply appreciated.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
___
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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Splitting Hubbard U directory question

[Vahid Askarpour]

Dear Iurii,

Thank you for your clear and detailed explanation. I have launched the 
calculations as you suggested and they are running fine.

Best,
Vahid

On Nov 22, 2021, at 6:08 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

The HP calculation can be split and parallelized. It depends how you want to do 
this. In example 7 of HP one needs to perturb two atoms, one Mn atom and one Ni 
atom. So we can split the HP calculation into two - in this case, we need to 
have different "outdir" for these two independent calculations, say TMP1 and 
TMP2.  You would need to run the PW calculations once (e.g. using TMP1) and 
then copy temporary files from TMP1 to TMP2. Then you run HP by perturbing Mn 
and using TMP1, and run HP by perturbing Ni and using TMP2. Once the 
calculation is finished successfully, you need to copy the output of TMP2/HP to 
TMP1/HP and then run the final step with  compute_hp = .true. and using TMP1.

On top of that, you can parallelize each calculation over q points using 
start_q, last_q, and sum_pertq. In this case, you would need to further split 
TMP1 into subfolders and TMP2 into subfolders, if you want to run this in 
parallel (if you run it sequentially, then no need to split TMP1 and TMP2 
subfolders).

I hope this clarifies a bit how to do it.

HTH

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Sunday, November 21, 2021 1:29:10 PM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Splitting Hubbard U directory question

In case anyone might be trying this, I ended up creating two self-consistent 
folders and ran step1.in in one and step2.in in the other.

Cheers,
Vahid

> On Nov 20, 2021, at 7:07 PM, Vahid Askarpour 
> mailto:vh261...@dal.ca>> wrote:
>
> Dear QE community,
>
> In the HP/examples/example07, the scf.in, step1.in and step2.in have the same 
> outdir as stated in the HP documentation which in this case is
>
> outdir='/scratch/timrov/WORK_DFPT_plus_U/A_PORTING_2018/A_Gitlab/A_my_Gitlab_08.11.2018/q-e/tempdir/'
>
> But when I run step1.in and step2.in at the same time in the outdir or in 
> separate folders, only one HP subfolder is create in the outdir where step1 
> and step2  jobs both write to this HP subfolder. How do I create different HP 
> subfolders for step1.in and step2.in?
>
> Thank you,
> Vahid
>
> Vahid Askarpour
> Department of physics and atmospheric science
> Dalhousie University
> Halifax, NS
> CANADA
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX 
> (www.max-centre.eu<http://www.max-centre.eu/>)
> users mailing list 
> users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] Splitting Hubbard U directory question

[Vahid Askarpour]

In case anyone might be trying this, I ended up creating two self-consistent 
folders and ran step1.in in one and step2.in in the other. 

Cheers,
Vahid

> On Nov 20, 2021, at 7:07 PM, Vahid Askarpour  wrote:
> 
> Dear QE community,
> 
> In the HP/examples/example07, the scf.in, step1.in and step2.in have the same 
> outdir as stated in the HP documentation which in this case is
> 
> outdir='/scratch/timrov/WORK_DFPT_plus_U/A_PORTING_2018/A_Gitlab/A_my_Gitlab_08.11.2018/q-e/tempdir/'
> 
> But when I run step1.in and step2.in at the same time in the outdir or in 
> separate folders, only one HP subfolder is create in the outdir where step1 
> and step2  jobs both write to this HP subfolder. How do I create different HP 
> subfolders for step1.in and step2.in?
> 
> Thank you,
> Vahid
> 
> Vahid Askarpour
> Department of physics and atmospheric science
> Dalhousie University
> Halifax, NS
> CANADA
> 
> 
> 
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
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[QE-users] Splitting Hubbard U directory question

[Vahid Askarpour]

Dear QE community,

In the HP/examples/example07, the scf.in, step1.in and step2.in have the same 
outdir as stated in the HP documentation which in this case is

outdir='/scratch/timrov/WORK_DFPT_plus_U/A_PORTING_2018/A_Gitlab/A_my_Gitlab_08.11.2018/q-e/tempdir/'

But when I run step1.in and step2.in at the same time in the outdir or in 
separate folders, only one HP subfolder is create in the outdir where step1 and 
step2  jobs both write to this HP subfolder. How do I create different HP 
subfolders for step1.in and step2.in?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA



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Re: [QE-users] Tag "loto_2d" in QE-6.8

[Vahid Askarpour]

I see. Thanks Paolo for this clarification.

Cheers,
Vahid

On Sep 16, 2021, at 4:55 AM, Paolo Giannozzi 
mailto:p.gianno...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
On Thu, Sep 16, 2021 at 12:13 AM Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

[...] in the online manual for ph.x 6.8, loto_2d is not described

it is not used by ph.x but by auxiliary codes matdyn.x, dynmat.x, q2r.x and 
described in their documentation. See also PHonon/examples/example17

Paolo

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

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[QE-users] Tag "loto_2d" in QE-6.8

[Vahid Askarpour]

Dear QE Community,

In line 127 of rigid.f90 in the Phonon package of QE-6.8, we see

IF (loto_2d) THEN

But in the online manual for ph.x 6.8, loto_2d is not described. Is this 
omission intentional? Is 2D splitting of LO-TO officially supported in the ph.x 
6.8?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

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[QE-users] Broken SOC in electron-phonon calculation in QE-6.8

[Vahid Askarpour]

The EPW forum kindly clarified that the issue is not with EPW but likely the 
PHonon code.

Cheers,
Vahid
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Re: [QE-users] reproducing phonon dispersion of FCC aluminum

[Vahid Askarpour]

If you refer to the sharp change in slope around K, you need to make a jump 
from K to U. These two points are equivalent. Attached please see one that I 
did a while back.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA



On Sep 9, 2021, at 1:24 PM, Paolo Giannozzi 
mailto:p.gianno...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
You mean: reproduce another calculation, or experiments? How is the 
"al.ph.bands.eps" graph obtained?

Anyway: I don't see anything wrong in the data, apart from self-consistency  
thresholds that are a little bit too large (setting thr_conv=1.0e-10 in the scf 
input and - more importantly - tr2_ph=1.0e-14 or smaller in the phonon input,  
improves the reliability of the calculation at the price of one second CPu or 
so).

Paolo

On Thu, Sep 9, 2021 at 5:36 AM Jacopo Simoni via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:
Dear QE users,
I am trying to reproduce the phonon dispersion of FCC aluminum, and overall 
looks correct except around the K point in the FBZ. I tried everything to solve 
the issue but I am not able to get rid of it.
I attach here the band plot, in addition I upload all the input SCF and PH 
calculations, I appreciate any suggestion.

Thanks in advance,
Jacopo Simoni, Lawrence Berkeley National Lab.
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

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phband.pdf
Description: phband.pdf
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[QE-users] Broken SOC in electron-phonon calculation in QE-6.8

[Vahid Askarpour]

Dear QE Community,

On the QE Github page, it states that for QE-6.8


  *   electron-phonon calculation in the non-colinear/spinorbit case is broken

Does this refer to electron-phonon calculation with the PHonon code or with the 
EPW code?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA
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Re: [QE-users] Regarding Relaxing atomic positions with version 6.8

[Vahid Askarpour]

Hi Konda,

I have had the same issue with the latest QE. I found that by running QE (under 
slurm) with the following command always avoids the cholesky issue:

srun pw.x -npools $SLURM_NTASKS < relax.in > relax.out

Don’t ask why because I do not know.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Aug 25, 2021, at 7:09 AM, Kondaiah Samudrala 
mailto:konda.phys...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Paolo,

This is happening for the past two months for every input structure with new 
intel compilers(2020). If I use internal lapack and blas, then the same input 
is running without any errors. But the computational time is very high while 
using internal lapack and blas.
If need I can share the inputs with you personally for the test run(PS: this 
work is going to publication). I am very confident about my input structure but 
somehow diagonalization process is having some issues (I am not a developer but 
frequent use. If I am wrong consider my apologies). Kindly help me in this 
regard

with Regards
Konda

Dr. Samudrala Appalakondaiah
Postdoctoral Researcher
Department of Physics,
University of Seoul, Seoul 02504
South Korea
Phone no : +821028514541
Google Scholar ID: 
https://scholar.google.co.in/citations?user=d8_gVLwJ&hl=en
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Re: [QE-users] Interpolation for 2D phonons results in one imaginary branch near Gamma

[Vahid Askarpour]

Hi Thomas,

This may not be directly related to your question and you may have already 
tried it but I found that for 2D materials, if in the vc-relax step, I ensure 
that the in-plane stresses are almost or exactly zero, I can make the flexural 
mode energies entirely positive along the various BZ segments. 

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

> On Jul 14, 2021, at 12:00 PM, Thomas Brumme  wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> Did anyone try recently the 2D cutoff technique for phonons? Is there
> maybe an error in my input?
> 
> Regards
> 
> Thomas
> 
> On 7/7/21 11:37 AM, Stefano Baroni wrote:
>> Oh, certo: scusa, dimenticavo. S.
>> 
>> --
>> Stefano Baroni, Trieste -- swift message written and sent on the go
>> 
>>> Il giorno 7 lug 2021, alle ore 10:42, Thomas Brumme 
>>>  ha scritto:
>>> 
>>> Dear all,
>>> 
>>> I think I don't see the wood for the trees and hope that someone can help.
>>> 
>>> I want to calculate the phonons for a 2D material using the 2D cutoff 
>>> technique. The scf calculations for the well-relaxed system work without a 
>>> problem and I also get no error calculating the phonons on a 5x5x1 q-point 
>>> grid. The relevant portions of the scf and phonon input are attached below. 
>>> All frequencies are positive at every single q point, except the 3 acoustic 
>>> branches at the Gamma point which are "only" -10 cm^-1 and -15 cm^-1. 
>>> However, the interpolation, in order to get the dispersion, results in one 
>>> branch which is negative for quite some portion near Gamma - for the first 
>>> half along G-K I have up to -130 cm^-1 and along G-M up to -60 cm^-1. I 
>>> guess that this is the out-of-plane acoustic branch and now I wonder if 
>>> this is real (i.e., the system is really unstable) or if I make some 
>>> obvious mistake. I will also check by explicitly calculating few q points 
>>> in the relevant region but before I wanted to ask here.
>>> 
>>> Any help would be appreciated!
>>> 
>>> Regards
>>> 
>>> Thomas Brumme
>>> 
>>> 
>>> scf:
>>> 
>>> &control
>>> calculation   = 'scf'
>>> prefix= 'pasc12',
>>> pseudo_dir= '/home/tbrumme/pseudos/pslibrary.1.0.0/rel-pbe/',
>>> outdir= '/scratch/ws/0/tbrumme-pasc/',
>>> verbosity = 'high',
>>> wf_collect= .true.,
>>> /
>>> 
>>> &system
>>>ibrav = 0,
>>>  nat = 14,
>>> ntyp = 3,
>>>  ecutwfc = 70.0,
>>>  ecutrho = 560,
>>> noncolin = .true.,
>>> lspinorb = .true.,
>>> vdw_corr = 'DFT-D',
>>> nbnd = 96,
>>>  assume_isolated = '2D',
>>> /
>>> 
>>> &electrons
>>>  conv_thr = 1.D-14,
>>> /
>>> 
>>> ATOMIC_SPECIES
>>> C 12.0 'C.rel-pbe-n-kjpaw_psl.1.0.0.UPF'
>>> P 30.973761 'P.rel-pbe-n-kjpaw_psl.1.0.0.UPF'
>>>As 74.921595 'As.rel-pbe-dn-kjpaw_psl.1.0.0.UPF'
>>> 
>>> ATOMIC_POSITIONS crystal
>>> ...
>>> 
>>> CELL_PARAMETERS angstrom
>>>  6.69668  0.0   0.0
>>> -3.348340 5.799495  0.0
>>>  0.0  0.0  15.0
>>> 
>>> K_POINTS automatic
>>>   25 25 1 0 0 0
>>> 
>>> 
>>> phonons:
>>> 
>>> Phonon dispersions for pasc12
>>>  &inputph
>>>   tr2_ph=1.0d-18,
>>>   prefix='pasc12',
>>>   ldisp=.true.,
>>>   nq1=5, nq2=5, nq3=1,
>>>   outdir='/scratch/ws/0/tbrumme-pasc/',
>>>   fildyn='pasc12.dyn.xml',
>>>   max_seconds = 83700,
>>>   verbosity='high',
>>>   recover=.true.
>>>   alpha_mix(1)=0.4,
>>>  /
>>> 
>>> 
>>> q2r and matdyn:
>>> 
>>> &input
>>>   fildyn='pasc12.dyn.xml', flfrc='pasc12.551.fc', loto_2d=.false., 
>>> zasr='simple',
>>> /
>>> 
>>> &input
>>> flfrc=&

Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Vahid Askarpour]

Dear Evgeniy,

I use the following  for my graphene dispersion. Please note that the actual 
coordinates depend on the PSP.

4
0.0 0.0 0.0 150 ! G
0.000  -0.577588 0.0 150 ! M
-0.3334706  -0.577588 0.0 150 ! K
0.0 0.0 0.0 1

So the matdyn.x code will automatically set 150 points between the first 2 
high-symmetry points and so on.

Cheers,
Vahid

On Mar 30, 2021, at 11:58 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

If we use the default values of the q_in_band_form variables, then how do we 
find intermediate points between the points of high symmetry, as for example on 
this site https://www.afs.enea.it/buonocor/graphane-with-phonon.html ? Are 
intermediate points always needed, we noticed that in some examples they are 
missing.

Thanks for the help.

Evgeniy Sysoev



30.03.2021, 17:28, "Vahid Askarpour" mailto:vh261...@dal.ca>>:
The coordinates of the high-symmetry points in matdyn.in should be in cartesian 
not crystal because you are specifying q_in_band_form=.true.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Mar 30, 2021, at 11:19 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Quantum Espresso experts,

I am having trouble calculating the phonon bands of graphene.

First, I took the cif-file of the already relaxed graphite cell from the 
Materials Project site https://next-gen.materialsproject.org/ and made graphene 
cell from it by hand.
Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
I used the same parameters to perform a scf calculation:

&CONTROL
calculation='scf'
title='graphene'
prefix='graphene'
verbosity='high'
restart_mode='from_scratch'
nstep=1000
iprint=1
tstress=.true.
tprnfor=.true.
disk_io='default'
pseudo_dir = '/home/mxm2/Desktop/Graphene',
outdir='/home/mxm2/Desktop/Graphene/temp'
/
&SYSTEM
ibrav = 0,
celldm(1)=1.889726,
nat = 2,
ntyp = 1,
ecutwfc = 60.0 ,
ecutrho = 480.0 ,
/
&ELECTRONS
electron_maxstep = 1000,
conv_thr = 1.0d-12 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7d0 ,
/
ATOMIC_SPECIES
C 12.011 C.pz-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
C0.0   0.0   0.000861580
C0.33000   0.67000   0.000838420
CELL_PARAMETERS (alat)
   2.438515837  -0.0   0.0
  -1.219257919   2.111816662   0.0
  -0.0  -0.0  19.995916314

K_POINTS automatic
12 12 1 0 0 0

Then, I run ph.in calculation:

&inputph
recover=.true.
tr2_ph=1.0d-14,
prefix='graphene',
ldisp=.true.
nq1=12,
nq2=12,
nq3=1,
amass(1)=12.011,
outdir='/home/mxm2/Desktop/Graphene/temp',
fildyn='graphene.dyn',
/

My q2r:

&input
fildyn='graphene.dyn',
zasr='simple',
flfrc='graphene.12x12x1.fc'
/

Matdyn input:

&input
asr='simple',
amass(1)=12.011,
flfrc='graphene.12x12x1.fc',
flfrq='graphene.disp.freq'
q_in_band_form=.true.,
/
4 ! number of q-points
0.000 0.000 0.000 10 ! gamma point
0.500 0.000 0.000 10 ! M
0.333 0.333 0.000 10 ! K
0.000 0.000 0.000  1 ! gamma point

Plotband:

graphene.disp.freq
0 1600
graphene.disp.freq.dat
graphene.disp.freq.ps
0
100 0

Why the phonon dispersion does not match the pictures from the papers and for 
calculations with e.g. 18x18x1 k-point and nq-point sets the output file of 
graphene.dyn1 look like:

Dielectric Tensor:

166.332153320312  0.
166.332275390625  0.
  0.  0.  1.116060253916

 Effective Charges E-U: Z_{alpha}{s,beta}

 atom #1
  -7471.575740195811 -0.002632206306  0.
 -0.002632205375-7471.5796640161420.
  0.  0. -0.003734609171

Also, what is the best way to set the lattice parameters, via Ibrav or 
CELL_PARAMETERS?
Any help is appreciated.

Best regards,
Evgeniy Sysoev.
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,

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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Vahid Askarpour]

The coordinates of the high-symmetry points in matdyn.in should be in cartesian 
not crystal because you are specifying q_in_band_form=.true.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Mar 30, 2021, at 11:19 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Quantum Espresso experts,

I am having trouble calculating the phonon bands of graphene.

First, I took the cif-file of the already relaxed graphite cell from the 
Materials Project site https://next-gen.materialsproject.org/ and made graphene 
cell from it by hand.
Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
I used the same parameters to perform a scf calculation:

&CONTROL
calculation='scf'
title='graphene'
prefix='graphene'
verbosity='high'
restart_mode='from_scratch'
nstep=1000
iprint=1
tstress=.true.
tprnfor=.true.
disk_io='default'
pseudo_dir = '/home/mxm2/Desktop/Graphene',
outdir='/home/mxm2/Desktop/Graphene/temp'
/
&SYSTEM
ibrav = 0,
celldm(1)=1.889726,
nat = 2,
ntyp = 1,
ecutwfc = 60.0 ,
ecutrho = 480.0 ,
/
&ELECTRONS
electron_maxstep = 1000,
conv_thr = 1.0d-12 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7d0 ,
/
ATOMIC_SPECIES
C 12.011 C.pz-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
C0.0   0.0   0.000861580
C0.33000   0.67000   0.000838420
CELL_PARAMETERS (alat)
   2.438515837  -0.0   0.0
  -1.219257919   2.111816662   0.0
  -0.0  -0.0  19.995916314

K_POINTS automatic
12 12 1 0 0 0

Then, I run ph.in calculation:

&inputph
recover=.true.
tr2_ph=1.0d-14,
prefix='graphene',
ldisp=.true.
nq1=12,
nq2=12,
nq3=1,
amass(1)=12.011,
outdir='/home/mxm2/Desktop/Graphene/temp',
fildyn='graphene.dyn',
/

My q2r:

&input
fildyn='graphene.dyn',
zasr='simple',
flfrc='graphene.12x12x1.fc'
/

Matdyn input:

&input
asr='simple',
amass(1)=12.011,
flfrc='graphene.12x12x1.fc',
flfrq='graphene.disp.freq'
q_in_band_form=.true.,
/
4 ! number of q-points
0.000 0.000 0.000 10 ! gamma point
0.500 0.000 0.000 10 ! M
0.333 0.333 0.000 10 ! K
0.000 0.000 0.000  1 ! gamma point

Plotband:

graphene.disp.freq
0 1600
graphene.disp.freq.dat
graphene.disp.freq.ps
0
100 0

Why the phonon dispersion does not match the pictures from the papers and for 
calculations with e.g. 18x18x1 k-point and nq-point sets the output file of 
graphene.dyn1 look like:

Dielectric Tensor:

166.332153320312  0.
166.332275390625  0.
  0.  0.  1.116060253916

 Effective Charges E-U: Z_{alpha}{s,beta}

 atom #1
  -7471.575740195811 -0.002632206306  0.
 -0.002632205375-7471.5796640161420.
  0.  0. -0.003734609171

Also, what is the best way to set the lattice parameters, via Ibrav or 
CELL_PARAMETERS?
Any help is appreciated.

Best regards,
Evgeniy Sysoev.
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Re: [QE-users] wrong phonon dispersion at K-point

[Vahid Askarpour]

In the matdyn.in file, the coordinates of the high-symmetry points should be in 
cartesian not crystal coordinates since you are using q_in_band_form=.true.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Jan 22, 2021, at 12:56 PM, Roozbeh Anvari 
mailto:roozbeh.anv...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.


Dear Quantum Espresso experts,

I am having a trouble calculating the phonon bands of graphene at $K$-point,

I am using NC+LDA and NC+PBE, ecutwfs=60, Ecutrho=400.0, forc_conv_thr=1.0d-6,

as you can see in the attached figure, the calculated acoustic and optical 
eigenvalues are ok at $\Gamma$ and $M$-points, however the calculated value 
deviates from what it should be at $K$-point:
TA and ZA branches are not overlapping at $K$-point,
and a strange bump can be seen when ZO approaches $K$-point,

I have checked the convergence for K-mesh, Ecutwfs, and Ecutrho,
I have also tried increasing the K and q mesh for scf-calculation,
using tr2_ph = 1E-14 and alpha_mix(niter)= .1 also does not improve the results,


Thank you for your help,
Regards,
Roozbeh
PDF, physics, Queen's university


Here is the setup I am using,

step 1, pw.x

&CONTROL

 calculation='scf'
 forc_conv_thr=1.0d-6,
/

&SYSTEM
ibrav=0, nat = 2, ntyp = 1,
ecutwfc = 60.0 , ecutrho = 400.0, ! 480
nosym=.true.,
occupations='smearing', smearing='cold', degauss=0.02
la2F = .true.,
   /

&ELECTRONS
startingwfc='random'
diagonalization='cg'
conv_thr = 1.0e-12
mixing_beta = 0.2
electron_maxstep=200


ATOMIC_SPECIES
C  12.011   C.pz-vbc.UPF

CELL_PARAMETERS (angstrom)
   2.428479517  -0.00605   0.0
  -1.214240282   2.103124989   0.0
   0.0   0.0  20.0

ATOMIC_POSITIONS (crystal)
C-0.00023157170.00023440990.4996978700
C 0.66642673430.33357040660.4996978902

K_POINTS automatic
64 64  1 0 0 0

%
%  step 2 ,pw.x
%

  same as above except
  la2F = .false.,
   K_POINTS automatic
32 32 1 0 0 0

%
%  step 3 , ph.x
%


 &inputph
  tr2_ph=1.0d-14,
  prefix='ml_gr',
  fildvscf='ml_gredv',
  amass(1)=12.011,
  outdir='./tmp',
  fildyn='ml_gr.dyn',
  electron_phonon='interpolated',
  !el_ph_sigma=0.005,
  !el_ph_nsigma=10,
  alpha_mix=0.1
  diagonalization='cg',
  trans=.true.,
  ldisp=.true.,
  nq1=4 , nq2=4, nq3=1
  ! nq1=8 , nq2=8, nq3=1   makes no difference
 /


%
%  step 4  , q2r.x
%

 &input
  zasr='simple',
  fildyn='ml_gr.dyn',
  flfrc='gr333.fc',
  la2F=.true.
 /


%
%  step 5 , matdyn.x
%

  &input
asr='simple',
amass(1)=12.011,
flfrc='gr333.fc',
flfrq='gr333.freq',
la2F=.true.,
dos=.false.
 q_in_band_form=.true.
 /
   4
0 0 0 20
0 .5 0 20
   -0.333  0.666  0. 20
0 0 0 1
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Re: [QE-users] Bi2Se3 vc-relax and band structure calculation

[Vahid Askarpour]

The atomic positions are specified in alat units for vc-relax. They appear to 
be in crystal coordinates.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS

On Nov 17, 2020, at 5:19 AM, Varrick Suezaki 
mailto:vsuez...@ucr.edu>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear PW users,
I'm trying to do a band structure calculation for bi2se3, but the resulting 
band structure does not look like other DFT calculations as it is missing the 
0.3eV band gap.  I also tried uploading my input file to SeeK-Path and the 
crystal structure looked wrong and deformed.  Below are my vc-relax and band 
input files, is there something I'm missing? I'm using v6.5 on a CentOS 8 
Vmware workstation (Sorry, new to DFT calculations).

&control
calculation = 'vc-relax'
prefix='bi2se3rel'
restart_mode = 'from_scratch'
outdir= '/home/name/QEoutput'
pseudo_dir='/home/name/quantum_espresso/q-e-qe-6.5/pseudo'
etot_conv_thr = 1e-7
forc_conv_thr = 1e-6
/
&system
ibrav = -5, celldm(1) = 18.6947, celldm(4) = 0.9135, nat = 5, ntyp = 3,
ecutwfc = 40, ecutrho = 500,
rhombohedral = .true.,
noncolin=.true.,lspinorb=.true.,starting_magnetization=0.,
nbnd=78,
vdw_corr = 'grimme-d2'
/
&electrons
conv_thr = 1.0e-9,
/
&ions
/
&cell
cell_dofree='ibrav'
/
ATOMIC_SPECIES
 Bi   208.98  Bi.rel-pbe-dn-rrkjus_psl.1.0.0.UPF
 Se1  78.96   Se.rel-pbe-dn-rrkjus_psl.1.0.0.UPF
 Se2  78.96   Se.rel-pbe-dn-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS (alat)
 Bi 0.3973 0.3973 0.3973  0 0 0
 Bi 0.6027 0.6027 0.6027  0 0 0
 Se10. 0. 0.  0 0 0
 Se20.2079 0.2079 0.2079  0 0 0
 Se20.7821 0.7821 0.7821  0 0 0
K_POINTS (automatic)
  8 8 8 0 0 0

&control
calculation = 'bands'
prefix='bi2se3rel'
restart_mode = 'from_scratch'
wf_collect=.true.,
verbosity='high',
outdir= '/home/name/QEoutput'
pseudo_dir='/home/name/quantum_espresso/q-e-qe-6.5/pseudo'
etot_conv_thr = 1e-5
forc_conv_thr = 1e-4
/
&system
ibrav = -5, celldm(1) = 18.6947, celldm(4) = 0.9135, nat = 5, ntyp = 3,
ecutwfc = 40, ecutrho = 500,
rhombohedral = .true.,
noncolin=.true.,lspinorb=.true.,starting_magnetization=0.,
nbnd=78,
vdw_corr = 'grimme-d2'
/
&electrons
conv_thr = 1.0e-8,
diago_full_acc=.true.,
/
ATOMIC_SPECIES
 Bi   208.98  Bi.rel-pbe-dn-rrkjus_psl.1.0.0.UPF
 Se1  78.96   Se.rel-pbe-dn-rrkjus_psl.1.0.0.UPF
 Se2  78.96   Se.rel-pbe-dn-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS crystal
 Bi 0.3973 0.3973 0.3973  0 0 0
 Bi 0.6027 0.6027 0.6027  0 0 0
 Se11. 1. 1.  0 0 0
 Se20.2079 0.2079 0.2079  0 0 0
 Se20.7821 0.7821 0.7821  0 0 0
K_POINTS crystal_b
5
 0.0  0.0  0.0 20 !gG
 0.5  0.5  0.5 20 !Z
 0.5  0.5 -0.0 20 !F
 0.0  0.0  0.0 20 !gG
 0.0  0.0 -0.5 20  !L1

Thank you,
Varrick Suezaki
Department of Physics and Astronomy
University of California, Riverside
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Re: [QE-users] Query regarding k path selection, mismatching of band gap

[Vahid Askarpour]

I think for insulators, occupation =fixed in the scf calculation. The degauss 
value is mainly for metals. You are using a broadening of 0.02Ry=0.272eV for a 
gap which is only 0.04eV. This broadening will likely result in a metallic DOS, 
which is what you are getting. For the nscf/DOS calculation, I suggest the 
tetrahedron method. These are explained in the QE manual.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS

On Oct 13, 2020, at 4:49 PM, Poonam Kaushik 
mailto:poonamkaushi...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Dear Expert,
About the first option, I used to confuse to select the correct option for the 
occupation, smearing type, and broadening part. In my input file, I used an 
'mv' smearing with a broadening of 0.02 Ry. So either I can reduce it to 0.01 
Ry or  I can try any other occupation,  like tetrahedra or fixed. my system is 
an insulator with a small bandgap of 0.04 eV. Also in the third option, I 
calculated the k path by using the CIF file, and k-pathfinder. Please correct 
me if I am wrong.

Thanks and regards,
Poonam Sharma




-
Poonam Sharma
Research Scholar
Department of Physics
Indian Institute of Technology Bombay
Mumbai - 400076
India.



On Wed, Oct 14, 2020 at 12:18 AM Nicola Marzari 
mailto:nicola.marz...@epfl.ch>> wrote:
On 13/10/2020 20:43, Poonam Kaushik wrote:
> Dear Expert,
> So the only option that I have is to include the complete path and do
> the calculation again.
> Thank you so much for your suggestion.
>

Mostly welcome, but you have three options - destiny can be generous
sometimes.

The first option would be doing a more careful DOS:
https://www.quantum-espresso.org/Doc/INPUT_DOS.html

nicola

>
>
> Thanks and regards,
> Poonam Sharma
>
>
>
>
> -
> Poonam Sharma
> Research Scholar
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
>
>
>
> On Tue, Oct 13, 2020 at 11:53 PM Nicola Marzari 
> mailto:nicola.marz...@epfl.ch>
> <mailto:nicola.marz...@epfl.ch<mailto:nicola.marz...@epfl.ch>>> wrote:
>
>
>
>
>   From the most to the less likely, it could be that your DOS has some
> broadening that masks the existence of a small gap, or that the gap
> closes across the last two segments of the path that you are
> missing, or
> that you are very unlucky and the band gaps closes at points that do
> not
> lie on a high symmetry path.
>
>   nicola
>
>
> On 13/10/2020 19:53, Poonam Kaushik wrote:
>  >
>  > Dear Experts,
>  >   I have one query regarding k path selection. After using Kpath
> finder
>  > (https://www.materialscloud.org/work/tools/seekpath ), i got
> this type
>  > of  k path
>  > G-M-K-G-A-L-H-A|L-M|H-K for my structure. In the calculation, I
> used, up
>  > to G-M-K-G-A-L-H-A. So, is this ok to select a path up to this?
>  > Basically in the band structure, I am getting some finite gap
> while in
>  > dos I m getting a zero bandgap, after selecting the path up to
>  > G-M-K-G-A-L-H-A. I am not able to figure out why this is happening?
>  > Should it help to include the complete path? I am attaching here my
>  > input file, band structure, and dos. Please have a look.
>  >
>  >
> https://drive.google.com/drive/folders/1UhUgod8KnvdovJfxMqbJMQwdtb3dE-yY
>  >
>  >   I'll be very thankful for any suggestions.
>  >
>  > Thanks and regards,
>  > Poonam Sharma
>  >
>  >
>  >
>  >
> 
> -
>  > Poonam Sharma
>  > Research Scholar
>  > Department of Physics
>  > Indian Institute of Technology Bombay
>  > Mumbai - 400076
>  > India.
>  >
>  >
>  > ___
>  > Quantum ESPRESSO is supported by MaX 
> (www.max-centre.eu<http://www.max-centre.eu/>
> <http://www.max-centre.eu<http://www.max-centre.eu/>>)
>  > users mailing list 
> users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>
> 
> <mailto:users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>>
>  > https://lists.quantum-es

Re: [QE-users] Band structure

[Vahid Askarpour]

It should be filband not filbands.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS

On Sep 28, 2020, at 1:29 PM, Menna Hasan 
mailto:menna.ha...@aucegypt.edu>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Ms. Pietro,
Thank you for your reply, I checked and nothing is wrong, here is the input 
file:

&BANDS
  prefix='TiO2'
  outdir='./'
  filbands='bands.dat'
/

On Mon, Sep 28, 2020 at 5:43 PM Pietro Delugas 
mailto:pdelu...@sissa.it>> wrote:

Hello

the program says there  is something wrong in your input.

Here's a small description of the namelist of bands.x,

https://www.quantum-espresso.org/Doc/INPUT_BANDS.html

jusy check that everything is correct and if you don;t find anything wrong  
post the input

greetings

Pietro

On 28/09/20 16:58, Menna Hasan wrote:
I am trying to run the band structure post processing but it keeps giving me 
this error: " Program BANDS v.6.3MaX starts on 28Sep2020 at 15:30:59

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
 "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
  URL 
http://www.quantum-espresso.org<http://www.quantum-espresso.org/>",
 in publications or presentations arising from this work. More details at
 http://www.quantum-espresso.org/quote

 Parallel version (MPI), running on 1 processors

 MPI processes distributed on 1 nodes

 %%
 Error in routine bands (5010):
 reading bands namelist
 %%

 stopping ...
"
I have tried all the commands suggested : bands.x <, -i and -inp
please advise.

Thanks



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Re: [QE-users] Hard PSP for copper

[Vahid Askarpour]

Just an update to my earlier email and hopefully a help to future users. I 
managed to generate a hard PSP not with the ld1.x code but with the Opium code. 
Although the PseudoDojo website does have a few hard PSPs, they are not hard 
enough. For Cu, the authors of PRB94, 155105 (2016) use a cutoff of 240Ry.

Cheers,
Vahid

> On Sep 14, 2020, at 8:56 AM, Vahid Askarpour  wrote:
> 
> Dear QE Community,
> 
> I am attempting to generate a hard PSP for copper (to calculate the 
> electrical conductivity of pure copper) by including the semi-core states as 
> done in the atomic code manual. The semi-core states are essential for a 
> correct evaluation of conductivity.
> 
> The spreads are:
> 
> s(3S/3S) =  1.00   =   0.7133   =0.5889  r(max) =   0.6112
> s(3P/3P) =  1.00   =   0.7502   =0.6671  r(max) =   0.6189
> s(3D/3D) =  1.00   =   1.0470   =1.5711  r(max) =   0.5961
> s(4S/4S) =  1.00   =   2.8937   =9.8815  r(max) =   2.2428
> 
> 
> My input file is:
> 
> &INPUT
>  title='Cu',
>  zed=29,
>  config='[Ar] 3d10 4s1',
>  rel=1,
>  dft='LDA'
>  iswitch=3,
>  nld=3,
>  rlderiv=2.41,
>  eminld=-10.0,
>  emaxld=4.0,
>  deld=0.01,
> /
> &INPUTP
>  pseudotype=2
>  lloc=0,
> ! rcloc=1.05
>  nlcc=.true.
>  file_pseudopw=‘Cu.UPF',
>  tm=.true.,
> /
> 3
> 3P  2  1  6.00   0.00  1.25  1.25  0.0
> 3D  3  2 10.00  0.00  1.05  1.05  0.0
> 3S  1  0  2.00   0.00  1.10  1.10  0.0
> &TEST
>  file_pseudo=‘Cu.UPF'
>  nconf=1
>  configts(1)='3s2 3p6 3d10 4s1'
>  ecutmin=50
>  ecutmax=500
>  decut=50
> /
> 
> In the output, I get
> 
> n l nl e AE (Ry)e PS (Ry)De AE-PS (Ry) 
> 1 0 3S   1( 2.00)   -8.38991   -8.38991   -0.0
> 2 1 3P   1( 6.00)   -5.29424   -5.294250.0
> 3 2 3D   1(10.00)  -0.39133   -0.391340.0
> 2 0 4S   1( 1.00)   -0.35756   -0.406140.04858  !
> 
> The 3S, 3P and 3D match. The last one does not but the manual says it might 
> not. 
> 
> The convergence is reached at
> 
> Cutoff (Ry) :  200.0
>   N = 1   N = 2   N = 3
> E(L=0) =-8.3893 Ry   -0.4061 Ry0.0005 Ry
> E(L=1) =-5.2513 Ry   -0.0602 Ry0.0230 Ry
> E(L=2) =-0.2263 Ry0.0347 Ry0.0793 Ry
> 
> Here 3P and 3D energies are off by 40 and 170mRy. Using P or D as reference 
> with proper lloc does not improve the energy discrepancy.
> 
> And if I use lloc=-1 with rcloc=1.05, I get
> 
> n l nl e AE (Ry)e PS (Ry)De AE-PS (Ry) 
> 1 0 3S   1( 2.00)   -8.38991   -8.38991   -0.0
> 2 1 3P   1( 6.00)   -5.29424   -5.294250.0
> 3 2 3D   1(10.00)  -0.39133   -0.391340.0
> 2 0 4S   1( 1.00)   -0.35756   -0.359960.00240
> 
> 4S energies look better. The convergence is reached at
> 
> Cutoff (Ry) :  200.0
>   N = 1   N = 2   N = 3
> E(L=0) =-8.3893 Ry   -0.3601 Ry0.0028 Ry
> E(L=1) =-5.2512 Ry   -0.0567 Ry0.0232 Ry
> E(L=2) =-0.2244 Ry0.0347 Ry0.0793 Ry
> 
> The 3P and 3D energies are still off by 40 and 170mRy. Changing rcloc from 
> 0.7 to 2.0 (which is too large) does not improve the energy differences for 
> these states.
> 
> It seems that regardless of the choice of lloc, the 3P and 3D energies remain 
> different. 
> 
> I have checked the consistency of the derivatives and wave functions but 
> despite the consistency, phonon calculation with convergence of even 10^-22 
> results in many negative frequencies not just at Gamma but at many other 
> q-points.
> 
> Is there a trick to making the 3P and 3D energies agree beyond what I have 
> already tried?
> 
> Thank you,
> 
> Vahid
> 
> Vahid Askarpour
> Department of physics and atmospheric science
> Dalhousie University
> Halifax, NS
> 
> 
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[QE-users] Hard PSP for copper

[Vahid Askarpour]

Dear QE Community,

I am attempting to generate a hard PSP for copper (to calculate the electrical 
conductivity of pure copper) by including the semi-core states as done in the 
atomic code manual. The semi-core states are essential for a correct evaluation 
of conductivity.

The spreads are:

 s(3S/3S) =  1.00   =   0.7133   =0.5889  r(max) =   0.6112
 s(3P/3P) =  1.00   =   0.7502   =0.6671  r(max) =   0.6189
 s(3D/3D) =  1.00   =   1.0470   =1.5711  r(max) =   0.5961
 s(4S/4S) =  1.00   =   2.8937   =9.8815  r(max) =   2.2428


My input file is:

&INPUT
  title='Cu',
  zed=29,
  config='[Ar] 3d10 4s1',
  rel=1,
  dft='LDA'
  iswitch=3,
  nld=3,
  rlderiv=2.41,
  eminld=-10.0,
  emaxld=4.0,
  deld=0.01,
/
&INPUTP
  pseudotype=2
  lloc=0,
 ! rcloc=1.05
  nlcc=.true.
  file_pseudopw=‘Cu.UPF',
  tm=.true.,
/
3
3P  2  1  6.00   0.00  1.25  1.25  0.0
3D  3  2 10.00  0.00  1.05  1.05  0.0
3S  1  0  2.00   0.00  1.10  1.10  0.0
&TEST
  file_pseudo=‘Cu.UPF'
  nconf=1
  configts(1)='3s2 3p6 3d10 4s1'
  ecutmin=50
  ecutmax=500
  decut=50
/

In the output, I get

 n l nl e AE (Ry)e PS (Ry)De AE-PS (Ry) 
 1 0 3S   1( 2.00)   -8.38991   -8.38991   -0.0
 2 1 3P   1( 6.00)   -5.29424   -5.294250.0
 3 2 3D   1(10.00)  -0.39133   -0.391340.0
 2 0 4S   1( 1.00)   -0.35756   -0.406140.04858  !

The 3S, 3P and 3D match. The last one does not but the manual says it might 
not. 

The convergence is reached at

 Cutoff (Ry) :  200.0
   N = 1   N = 2   N = 3
 E(L=0) =-8.3893 Ry   -0.4061 Ry0.0005 Ry
 E(L=1) =-5.2513 Ry   -0.0602 Ry0.0230 Ry
 E(L=2) =-0.2263 Ry0.0347 Ry0.0793 Ry

Here 3P and 3D energies are off by 40 and 170mRy. Using P or D as reference 
with proper lloc does not improve the energy discrepancy.

And if I use lloc=-1 with rcloc=1.05, I get

 n l nl e AE (Ry)e PS (Ry)De AE-PS (Ry) 
 1 0 3S   1( 2.00)   -8.38991   -8.38991   -0.0
 2 1 3P   1( 6.00)   -5.29424   -5.294250.0
 3 2 3D   1(10.00)  -0.39133   -0.391340.0
 2 0 4S   1( 1.00)   -0.35756   -0.359960.00240

4S energies look better. The convergence is reached at

 Cutoff (Ry) :  200.0
   N = 1   N = 2   N = 3
 E(L=0) =-8.3893 Ry   -0.3601 Ry0.0028 Ry
 E(L=1) =-5.2512 Ry   -0.0567 Ry0.0232 Ry
 E(L=2) =-0.2244 Ry0.0347 Ry0.0793 Ry

The 3P and 3D energies are still off by 40 and 170mRy. Changing rcloc from 0.7 
to 2.0 (which is too large) does not improve the energy differences for these 
states.

It seems that regardless of the choice of lloc, the 3P and 3D energies remain 
different. 

I have checked the consistency of the derivatives and wave functions but 
despite the consistency, phonon calculation with convergence of even 10^-22 
results in many negative frequencies not just at Gamma but at many other 
q-points.

Is there a trick to making the 3P and 3D energies agree beyond what I have 
already tried?

Thank you,

Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS


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Re: [QE-users] Need a script that can convert primitive cell file file using conventional cell cif file

[Vahid Askarpour]

I put your cif file into the MaterialsCloud input file generator 
(https://www.materialscloud.org/work/tools/qeinputgenerator). It returned the 
following QE input file:

&CONTROL
  calculation = 'scf'
  etot_conv_thr =   1.00d-04
  forc_conv_thr =   1.00d-04
  outdir = './out/'
  prefix = 'aiida'
  pseudo_dir = './pseudo/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/
&SYSTEM
  degauss =   1.4699723600d-02
  ecutrho =   2.40d+02
  ecutwfc =   5.00d+01
  ibrav = 0
  nat = 10
  ntyp = 4
  occupations = 'smearing'
  smearing = 'cold'
/
&ELECTRONS
  conv_thr =   2.00d-09
  electron_maxstep = 80
  mixing_beta =   4.00d-01
/
ATOMIC_SPECIES
Ag 107.8682 Ag_ONCV_PBE-1.0.oncvpsp.upf
Au 196.966569 Au_ONCV_PBE-1.0.oncvpsp.upf
Br 79.904 br_pbe_v1.4.uspp.F.UPF
Cs 132.9054519 Cs_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS crystal
Ag   0.50   0.50   0.50
Au   0.00   0.00   0.00
Br   0.752924   0.752924   0.247076
Br   0.247076   0.752924   0.752924
Br   0.247076   0.247076   0.752924
Br   0.752924   0.247076   0.752924
Br   0.247076   0.752924   0.247076
Br   0.752924   0.247076   0.247076
Cs   0.25   0.25   0.25
Cs   0.75   0.75   0.75
K_POINTS automatic
5 5 5 0 0 0
CELL_PARAMETERS angstrom
 -5.489549  -5.489549   0.00
 -5.489549   0.00  -5.489549
 -0.00  -5.4895490000  -5.489549

This seems to be a primitive cell.

Cheers,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada



On Jul 17, 2020, at 11:11 AM, Lorenzo Paulatto 
mailto:paul...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Hello,
as far as I know, cif2cell produces the primitive cell by default if it
can find it, apparently in this case it cannot. Anyway, you can always
do it by hand, it is a bit boring but in the worst case it will only
take a few hours.

cheers

On 7/17/20 4:04 PM, rekha sharma wrote:
Dear Prof. Lorenzo
cif2cell seems to be easy to use.
I have downloaded the Cs2AgAuBr6 from materials project (cif file is
attached herewith) but I do not find the primitive cell from it.
I used as
cif2cell Cs2AgAuBr6-conv.cif

I am getting 40 atoms as is in conventional one.

Could you tell me how to convert the attached cif file to a primitive
one using cif2cell?

Thank you very much.
Rekha

On Fri, Jul 17, 2020 at 4:31 PM Lorenzo Paulatto 
mailto:paul...@gmail.com>
<mailto:paul...@gmail.com>> wrote:

   I normally use cif2cell¹, it can produce conventional or primitive cell
   from a cif file. The I usually convert the Cartesian cell axes to ibrav
   using scan_ibrav.x (PW/tools), or by hand if it is easy

   hth


   [1]Comput. Phys. Commun. 182, 1183 (2011)

   On 7/16/20 4:10 PM, rekha sharma wrote:
> Dear Expert Users,
>
> It is possible that this question has been answered many times
   before
> but I could not find it on the forum.
>
> I have few complex structures and it is not possible to handle on my
> system in the conventional form.
>
> Can you please advise any tool that can help me to convert
> a conventional cell cif file to a primitive cell file?
>
> I have tried with VEST (niggli cell reduction) but it does not
   work for me.
>
> Thank you very much.
> Rekha
>
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   <http://www.max-centre.eu/quantum-espresso>)
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>

   --
   Lorenzo Paulatto - Paris
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--




Best wishes

Ms. Rekha
Teaching Assistant,
Department of Physics
RK college, Jaipur, India
Mob.: +11 90-95 790 71 697
Email: rekha1997...@gmail.com&

[QE-users] Need a script that can convert primitive cell file file using conventional cell cif file

[Vahid Askarpour]

I use the code FINDSYM (https://stokes.byu.edu/iso/findsym.php) which takes a 
cif file (of conventional or primitive cells) and output the primitive cell 
parameters. Can be used online or downloaded.

Cheers,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada

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Re: [QE-users] P=********** in the output directory of quantum espresso users.

[Vahid Askarpour]

The pressure is too large, which is why it is printed as stars.

You are only relaxing the atoms not the lattice constants. Is there a reason 
why you are not using vc-relax?

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada

> On Jun 19, 2020, at 10:52 AM, BENYAHIA NEZHA  
> wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> Dear QE users,
> 
> i have created a supercell of GaN-ZnO and i've tried to optimise it  using 
> the input file attached below.  however i receive in the output file a 
> pressure of  P=** and the convergence has been achieved. i used PAW 
> pseudopotential.
> 
> I would be very grateful if somebody helps or give suggestions.
> 
> 
> &CONTROL
>calculation   = "relax"
>etot_conv_thr =  1.0e-04
>forc_conv_thr =  1.0e-05
>outdir= "./tmp/"
>prefix= "GaN-ZnO4h"
>pseudo_dir= "../pseudo"
>restart_mode  = "from_scratch"
>tprnfor   = .TRUE.
>tstress   = .TRUE.
> /
> 
> &SYSTEM
>a   =  3.60
>c   =  40
>ecutrho =  7.2e+02
>ecutwfc =  1.0e+01
>ibrav   = 4
>nat = 32
>ntyp= 4
>occupations = "smearing"
>smearing= "gaussian"
>degauss  =0.02,
> /
> 
> &ELECTRONS
>conv_thr =  1.0e-07
>diagonalization  = "david"
>mixing_beta  =  3.0e-01
> /
> 
> &IONS
>ion_dynamics = "bfgs"
> /
> 
> &CELL
> /
> 
> K_POINTS {automatic}
> 4 4 1  0 0 0
> 
> ATOMIC_SPECIES
> Ga 69.72300  Ga.pz.UPF
> N  14.00680  N.pz.UPF
> Zn 65.39000  Zn.pz.UPF
> O  15.99940  O.pz.UPF
> 
> ATOMIC_POSITIONS {crystal}
> Ga  0.00   0.00   0.00
> Ga  0.68   0.34   0.125000
> Ga  0.34   0.68   0.187500
> Ga  0.34   0.68   0.062500
> N   0.00   0.00   0.046875
> N   0.68   0.34   0.171875
> N   0.34   0.68   0.234375
> N   0.34   0.68   0.109375
> Ga  0.00   0.00   0.25
> Ga  0.68   0.34   0.375000
> Ga  0.34   0.68   0.437500
> Ga  0.34   0.68   0.312500
> N   0.00   0.00   0.296875
> N   0.68   0.34   0.421875
> N   0.34   0.68   0.484375
> N   0.34   0.68   0.359375
> Zn  0.00   0.00   0.50
> Zn  0.68   0.34   0.625000
> Zn  0.34   0.68   0.687500
> Zn  0.34   0.68   0.562500
> O   0.00   0.00   0.546875
> O   0.68   0.34   0.671875
> O   0.34   0.68   0.734375
> O   0.34   0.68   0.609375
> Zn  0.00   0.00   0.75
> Zn  0.68   0.34   0.875000
> Zn  0.34   0.68   0.937500
> Zn  0.34   0.68   0.812500
> O   0.00   0.00   0.796875
> O   0.68   0.34   0.921875
> O   0.34   0.68   0.984375
> O   0.34   0.68   0.859375
> 
> 
> BENYAHIA NEZHA
> PhD Student in Materials Science
> LPMF-USTO
> Algeria
> 
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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] I don't know how to add empty bands and broaden my super cell

[Vahid Askarpour]

   9.305080   1.281057  12.260473
N   0.977921   5.774502  12.260473
N   5.141501   5.774502  12.260473
N   9.305080   5.774502  12.260473
N   0.977921  10.267946  12.260473
N   5.141501  10.267946  12.260473
N   9.305080  10.267946  12.260473
W   0.977921   3.447032  12.207706
W   5.141501   3.447032  12.207706
W   9.305080   3.447032  12.207706
W   0.977921   7.940476  12.207706
W   5.141501   7.940476  12.207706
W   9.305080   7.940476  12.207706
W   0.977921  -1.046412  12.207706
W   5.141501  -1.046412  12.207706
W   9.305080  -1.046412  12.207706
N   3.059711   1.252012  10.422372  0 0 0
N   7.223291   1.252012  10.422372  0 0 0
N  11.386870   1.252012  10.422372  0 0 0
N   3.059711   5.745456  10.422372  0 0 0
N   7.223291   5.745456  10.422372  0 0 0
N  11.386870   5.745456  10.422372  0 0 0
N   3.059711  10.238900  10.422372  0 0 0
N   7.223291  10.238900  10.422372  0 0 0
N  11.386870  10.238900  10.422372  0 0 0
W   3.059711   3.461867  10.333236  0 0 0
W   7.223291   3.461867  10.333236  0 0 0
W  11.386870   3.461867  10.333236  0 0 0
W   3.059711   7.955311  10.333236  0 0 0
W   7.223291   7.955311  10.333236  0 0 0
W  11.386870   7.955311  10.333236  0 0 0
W   3.059711  -1.031577  10.333236  0 0 0
W   7.223291  -1.031577  10.333236  0 0 0
W  11.386870  -1.031577  10.333236  0 0 0
N   0.977921   3.944664  10.052766  0 0 0
N   5.141501   3.944664  10.052766  0 0 0
N   9.305080   3.944664  10.052766  0 0 0
N   0.977921   8.438108  10.052766  0 0 0
N   5.141501   8.438108  10.052766  0 0 0
N   9.305080   8.438108  10.052766  0 0 0
N   0.977921  -0.548780  10.052766  0 0 0
N   5.141501  -0.548780  10.052766  0 0 0
N   9.305080  -0.548780  10.052766  0 0 0
W   0.977921   1.617195  10.00  0 0 0
W   5.141501   1.617195  10.00  0 0 0
W   9.305080   1.617195  10.00  0 0 0
W   0.977921   6.110639  10.00  0 0 0
W   5.141501   6.110639  10.00  0 0 0
W   9.305080   6.110639  10.00  0 0 0
W   0.977921  10.604083  10.00  0 0 0
W   5.141501  10.604083  10.00  0 0 0
W   9.305080  10.604083  10.00  0 0 0
C   7.223291   2.628097  19.75
H   6.590292   1.997000  20.383000
H   7.856291   1.997000  19.117000
H   6.590292   3.263000  19.117000
H   7.856291   3.263000  20.383000



On Wed, 17 Jun 2020 at 19:51, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:
Specify nbnd for bands.
For broadening, check the input parameters occupations, smearing, degauss.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada

On Jun 17, 2020, at 8:44 PM, Coralie Khabbaz 
mailto:khabbaz.cora...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
I am performing an SCF calculation (on a tungsten nitride slab that contains 
114 atoms) that is not converging. I was told that I had to add a few empty 
bands and a broadening. However, I don't know how to do that as I am still a 
beginner. How do I add empty bands and how do I broaden? Please help!!
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Re: [QE-users] I don't know how to add empty bands and broaden my super cell

[Vahid Askarpour]

Specify nbnd for bands.
For broadening, check the input parameters occupations, smearing, degauss.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada

On Jun 17, 2020, at 8:44 PM, Coralie Khabbaz 
mailto:khabbaz.cora...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
I am performing an SCF calculation (on a tungsten nitride slab that contains 
114 atoms) that is not converging. I was told that I had to add a few empty 
bands and a broadening. However, I don't know how to do that as I am still a 
beginner. How do I add empty bands and how do I broaden? Please help!!
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https://lists.quantum-espresso.org/mailman/listinfo/users

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[QE-users] Core electron energy

[Vahid Askarpour]

Dear QE Users,

Is it possible to output the core electron energy  with QE? I am hoping to use 
the core energy as a reference for electronic band shifts as a result of atomic 
displacement.

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada
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Re: [QE-users] Born charges of PbS

[Vahid Askarpour]

Hi Pietro,

Thank you for taking the time to respond. This has been a very enlightening 
discussion for me. I will try the Wannier code and see what I get.

Best wishes,
Vahid

On Apr 16, 2020, at 3:52 AM, Pietro Delugas 
mailto:pdelu...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Hi Vahid

In principle all occupied bands could contribute to the big difference  between 
 the dynamical charges and the oxydation numbers. How much they contribute  
depends on their polarizability. And I agree with you that following what I 
said about the behavior of the S-3p  band, the Pb-6s should contribute in the 
opposite direction, but first they are only 2 electrons/cell against 8 and 
also, I may be wrong, but I would expect the S 3p to be more polarizable.

If you are  curious about the detailed contributions to the dynamical charge 
anomaly from each  band  you could try to compute them with wannier90 for 
example.

regards Pietro


On 15/04/20 15:05, Vahid Askarpour wrote:
Hi Pietro,

If I understand your argument correctly, then the same can be said of the 2 
electrons of s-Pb localized just above 0eV. These 2 electrons are mainly 
centered on Pb, hybridized with other orbitals and move with Pb (in addition to 
10 d-electrons). So the dynamical charge for Pb is ~ -12. Adding zv gives a 
Born charge of ~2. The PHONON code gives a value of 4.122. So somehow, the 2 
electrons from s-Pb should move with sulphur and be loosely attached to Pb as 
noted by Stefano. The DOS does not seem to support this idea.

Thanks,
Vahid

On Apr 15, 2020, at 3:23 AM, Pietro Delugas 
mailto:pdelu...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Hello

from the pdos  2 electrons have moved from Pb 6p to fill the S 3p band, as 
expected.

The 3p band is hybridized with 6s and 6p orbitals of Pb and vice versa. So the 
S 3p is still made by orbitals centered on S ions but is spread to neighboring 
Pb ions. If a S ion is displaced it goes closer to some Pb ion and far from 
others, same thing happens dispacing a Pb.  As Stefano wrote the 3p orbitals 
would still be centered close to the S ion, Bader charge thus would  not 
change,  but the orbital will now   lean towards the closer Pb and away from 
those that are now a little bit farther,   this enhances the dynamical charge 
with respect to the oxidation number.

Pietro


On 14/04/20 00:54, Vahid Askarpour wrote:
The attached projected DOS for PbS suggests that the Pb s- and p- states have 
significant DOS and so perhaps the 4 electrons of Pb have not moved to sulphur 
unless I am reading the DOS incorrectly. The Pb d-states are lower in energy 
and not shown.

Cheers,
Vahid



On Apr 13, 2020, at 12:53 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear Stefano,

Thank you for this quick response. I was following Xavier Gonze’s argument in 
PRB58, 6224 (1998) Eq. 20 where

Z*(u)=dp/du, where p is the dipole moment and u is the displacement. Since 
p=u.Z(u), we get

Z*(u)=Z(u)+udZ(u)/du, where Z(u) is the static charge.

So here the Born charge is given in terms of change in charge.

I will try the projected DOS to see if the charge transfer is actually that 
large.

Best,
Vahid

On Apr 13, 2020, at 12:35 PM, Stefano de Gironcoli 
mailto:degir...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

I didnt follow completely your argument about the Bader charge but what
one should keep in mind is that the effective charge is the change in
polarization due to displacement not the change in charge...

think of a core electron shell (as the d orbitals of Pb can
approximately be considered) ... as you move the atom they follow
rigidly (that would make a contribution of 10 not far from your estimate).

from the PHONON result it looks like Pb gave away 4 all its valence
electrons to S. or rather they are so weakly bound to Pb that they don't
follow it, even if they can still belong its Bader volume.

it looks a bit extreme but this appears to be the result. You could
compute the atomic projected density of states and see if this seems the
case.

stefano

On 13/04/20 17:11, Vahid Askarpour wrote:
Dear QE Community,

I have calculated the Born charges using the PHONON code for PbS. The only 
non-zero elements are the diagonal ones and are 4.122 and -4.168, respectively.

In the zstar_eu.f90, Born charges consist of two terms as seen below: a part 
due to polarization calculation (dynamic) and the other is zv (static) which is 
the z_valence according to read_upf_v2.f90.

do ipol = 1, 3
do na = 1, nat
   zstareu (ipol, ipol, na) = zstareu (ipol, ipol, na) + zv (ityp ( na) )
enddo
 enddo

The zv values for Pb and S are 14 and 6 given in the PSP. If we subtract zv 
from the Born charges, we get the term due to polarization: -9.878 and -10.168. 
These values seem too large because of the argument below.

To estimate the polarization term, I reduce

Re: [QE-users] Born charges of PbS

[Vahid Askarpour]

Hi Pietro,

If I understand your argument correctly, then the same can be said of the 2 
electrons of s-Pb localized just above 0eV. These 2 electrons are mainly 
centered on Pb, hybridized with other orbitals and move with Pb (in addition to 
10 d-electrons). So the dynamical charge for Pb is ~ -12. Adding zv gives a 
Born charge of ~2. The PHONON code gives a value of 4.122. So somehow, the 2 
electrons from s-Pb should move with sulphur and be loosely attached to Pb as 
noted by Stefano. The DOS does not seem to support this idea.

Thanks,
Vahid

On Apr 15, 2020, at 3:23 AM, Pietro Delugas 
mailto:pdelu...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

Hello

from the pdos  2 electrons have moved from Pb 6p to fill the S 3p band, as 
expected.

The 3p band is hybridized with 6s and 6p orbitals of Pb and vice versa. So the 
S 3p is still made by orbitals centered on S ions but is spread to neighboring 
Pb ions. If a S ion is displaced it goes closer to some Pb ion and far from 
others, same thing happens dispacing a Pb.  As Stefano wrote the 3p orbitals 
would still be centered close to the S ion, Bader charge thus would  not 
change,  but the orbital will now   lean towards the closer Pb and away from 
those that are now a little bit farther,   this enhances the dynamical charge 
with respect to the oxidation number.

Pietro


On 14/04/20 00:54, Vahid Askarpour wrote:
The attached projected DOS for PbS suggests that the Pb s- and p- states have 
significant DOS and so perhaps the 4 electrons of Pb have not moved to sulphur 
unless I am reading the DOS incorrectly. The Pb d-states are lower in energy 
and not shown.

Cheers,
Vahid



On Apr 13, 2020, at 12:53 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear Stefano,

Thank you for this quick response. I was following Xavier Gonze’s argument in 
PRB58, 6224 (1998) Eq. 20 where

Z*(u)=dp/du, where p is the dipole moment and u is the displacement. Since 
p=u.Z(u), we get

Z*(u)=Z(u)+udZ(u)/du, where Z(u) is the static charge.

So here the Born charge is given in terms of change in charge.

I will try the projected DOS to see if the charge transfer is actually that 
large.

Best,
Vahid

On Apr 13, 2020, at 12:35 PM, Stefano de Gironcoli 
mailto:degir...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

I didnt follow completely your argument about the Bader charge but what
one should keep in mind is that the effective charge is the change in
polarization due to displacement not the change in charge...

think of a core electron shell (as the d orbitals of Pb can
approximately be considered) ... as you move the atom they follow
rigidly (that would make a contribution of 10 not far from your estimate).

from the PHONON result it looks like Pb gave away 4 all its valence
electrons to S. or rather they are so weakly bound to Pb that they don't
follow it, even if they can still belong its Bader volume.

it looks a bit extreme but this appears to be the result. You could
compute the atomic projected density of states and see if this seems the
case.

stefano

On 13/04/20 17:11, Vahid Askarpour wrote:
Dear QE Community,

I have calculated the Born charges using the PHONON code for PbS. The only 
non-zero elements are the diagonal ones and are 4.122 and -4.168, respectively.

In the zstar_eu.f90, Born charges consist of two terms as seen below: a part 
due to polarization calculation (dynamic) and the other is zv (static) which is 
the z_valence according to read_upf_v2.f90.

do ipol = 1, 3
do na = 1, nat
   zstareu (ipol, ipol, na) = zstareu (ipol, ipol, na) + zv (ityp ( na) )
enddo
 enddo

The zv values for Pb and S are 14 and 6 given in the PSP. If we subtract zv 
from the Born charges, we get the term due to polarization: -9.878 and -10.168. 
These values seem too large because of the argument below.

To estimate the polarization term, I reduce the alat by 1% and relax the atoms. 
This shifts the atoms from the unstrained position. I calculate the Bader 
charges for the unstrained and the strained cases. The change in the Bader 
charge is related to the atomic displacement. I have also tried keeping alat 
fixed and moving the atoms by 1%.

For unstrained PbS, the Bader charges are 12.998 and 7.001.
For the strained PbS, they are 13.004 and 6.995.

So a ~1% change in atomic positions results in a +/-0.006 change in Bader 
charge. From this calculation, I expect the contribution from polarization to 
be u(dZ/du), where u is interatomic distance, which amount to +0.6 for Pb and 
-0.6 for S.

The contribution from polarization I get (0.6 and -0.6) are quite different 
from the those of the PHONON code (-9.878 and -10.168). I am assuming that the 
code is correct and my logic is flawed. I would appreciate any thoughts you may 
have on this discrepancy.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie Univer

Re: [QE-users] Born charges of PbS

[Vahid Askarpour]

The attached projected DOS for PbS suggests that the Pb s- and p- states have 
significant DOS and so perhaps the 4 electrons of Pb have not moved to sulphur 
unless I am reading the DOS incorrectly. The Pb d-states are lower in energy 
and not shown.

Cheers,
Vahid



On Apr 13, 2020, at 12:53 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear Stefano,

Thank you for this quick response. I was following Xavier Gonze’s argument in 
PRB58, 6224 (1998) Eq. 20 where

Z*(u)=dp/du, where p is the dipole moment and u is the displacement. Since 
p=u.Z(u), we get

Z*(u)=Z(u)+udZ(u)/du, where Z(u) is the static charge.

So here the Born charge is given in terms of change in charge.

I will try the projected DOS to see if the charge transfer is actually that 
large.

Best,
Vahid

On Apr 13, 2020, at 12:35 PM, Stefano de Gironcoli 
mailto:degir...@sissa.it>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.

I didnt follow completely your argument about the Bader charge but what
one should keep in mind is that the effective charge is the change in
polarization due to displacement not the change in charge...

think of a core electron shell (as the d orbitals of Pb can
approximately be considered) ... as you move the atom they follow
rigidly (that would make a contribution of 10 not far from your estimate).

from the PHONON result it looks like Pb gave away 4 all its valence
electrons to S. or rather they are so weakly bound to Pb that they don't
follow it, even if they can still belong its Bader volume.

it looks a bit extreme but this appears to be the result. You could
compute the atomic projected density of states and see if this seems the
case.

stefano

On 13/04/20 17:11, Vahid Askarpour wrote:
Dear QE Community,

I have calculated the Born charges using the PHONON code for PbS. The only 
non-zero elements are the diagonal ones and are 4.122 and -4.168, respectively.

In the zstar_eu.f90, Born charges consist of two terms as seen below: a part 
due to polarization calculation (dynamic) and the other is zv (static) which is 
the z_valence according to read_upf_v2.f90.

do ipol = 1, 3
do na = 1, nat
   zstareu (ipol, ipol, na) = zstareu (ipol, ipol, na) + zv (ityp ( na) )
enddo
 enddo

The zv values for Pb and S are 14 and 6 given in the PSP. If we subtract zv 
from the Born charges, we get the term due to polarization: -9.878 and -10.168. 
These values seem too large because of the argument below.

To estimate the polarization term, I reduce the alat by 1% and relax the atoms. 
This shifts the atoms from the unstrained position. I calculate the Bader 
charges for the unstrained and the strained cases. The change in the Bader 
charge is related to the atomic displacement. I have also tried keeping alat 
fixed and moving the atoms by 1%.

For unstrained PbS, the Bader charges are 12.998 and 7.001.
For the strained PbS, they are 13.004 and 6.995.

So a ~1% change in atomic positions results in a +/-0.006 change in Bader 
charge. From this calculation, I expect the contribution from polarization to 
be u(dZ/du), where u is interatomic distance, which amount to +0.6 for Pb and 
-0.6 for S.

The contribution from polarization I get (0.6 and -0.6) are quite different 
from the those of the PHONON code (-9.878 and -10.168). I am assuming that the 
code is correct and my logic is flawed. I would appreciate any thoughts you may 
have on this discrepancy.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada
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PbS_pdos.pdf
Description: PbS_pdos.pdf
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Re: [QE-users] Born charges of PbS

[Vahid Askarpour]

Dear Stefano,

Thank you for this quick response. I was following Xavier Gonze’s argument in 
PRB58, 6224 (1998) Eq. 20 where 

Z*(u)=dp/du, where p is the dipole moment and u is the displacement. Since 
p=u.Z(u), we get

Z*(u)=Z(u)+udZ(u)/du, where Z(u) is the static charge.

So here the Born charge is given in terms of change in charge.

I will try the projected DOS to see if the charge transfer is actually that 
large.

Best,
Vahid

> On Apr 13, 2020, at 12:35 PM, Stefano de Gironcoli  wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> I didnt follow completely your argument about the Bader charge but what
> one should keep in mind is that the effective charge is the change in
> polarization due to displacement not the change in charge...
> 
> think of a core electron shell (as the d orbitals of Pb can
> approximately be considered) ... as you move the atom they follow
> rigidly (that would make a contribution of 10 not far from your estimate).
> 
> from the PHONON result it looks like Pb gave away 4 all its valence
> electrons to S. or rather they are so weakly bound to Pb that they don't
> follow it, even if they can still belong its Bader volume.
> 
> it looks a bit extreme but this appears to be the result. You could
> compute the atomic projected density of states and see if this seems the
> case.
> 
> stefano
> 
> On 13/04/20 17:11, Vahid Askarpour wrote:
>> Dear QE Community,
>> 
>> I have calculated the Born charges using the PHONON code for PbS. The only 
>> non-zero elements are the diagonal ones and are 4.122 and -4.168, 
>> respectively.
>> 
>> In the zstar_eu.f90, Born charges consist of two terms as seen below: a part 
>> due to polarization calculation (dynamic) and the other is zv (static) which 
>> is the z_valence according to read_upf_v2.f90.
>> 
>>  do ipol = 1, 3
>>  do na = 1, nat
>> zstareu (ipol, ipol, na) = zstareu (ipol, ipol, na) + zv (ityp ( na) 
>> )
>>  enddo
>>   enddo
>> 
>> The zv values for Pb and S are 14 and 6 given in the PSP. If we subtract zv 
>> from the Born charges, we get the term due to polarization: -9.878 and 
>> -10.168. These values seem too large because of the argument below.
>> 
>> To estimate the polarization term, I reduce the alat by 1% and relax the 
>> atoms. This shifts the atoms from the unstrained position. I calculate the 
>> Bader charges for the unstrained and the strained cases. The change in the 
>> Bader charge is related to the atomic displacement. I have also tried 
>> keeping alat fixed and moving the atoms by 1%.
>> 
>> For unstrained PbS, the Bader charges are 12.998 and 7.001.
>> For the strained PbS, they are 13.004 and 6.995.
>> 
>> So a ~1% change in atomic positions results in a +/-0.006 change in Bader 
>> charge. From this calculation, I expect the contribution from polarization 
>> to be u(dZ/du), where u is interatomic distance, which amount to +0.6 for Pb 
>> and -0.6 for S.
>> 
>> The contribution from polarization I get (0.6 and -0.6) are quite different 
>> from the those of the PHONON code (-9.878 and -10.168). I am assuming that 
>> the code is correct and my logic is flawed. I would appreciate any thoughts 
>> you may have on this discrepancy.
>> 
>> Thank you,
>> Vahid
>> 
>> 
>> Vahid Askarpour
>> Department of physics and atmospheric science
>> Dalhousie University
>> Halifax, NS
>> Canada
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[QE-users] Born charges of PbS

[Vahid Askarpour]

Dear QE Community,

I have calculated the Born charges using the PHONON code for PbS. The only 
non-zero elements are the diagonal ones and are 4.122 and -4.168, respectively.

In the zstar_eu.f90, Born charges consist of two terms as seen below: a part 
due to polarization calculation (dynamic) and the other is zv (static) which is 
the z_valence according to read_upf_v2.f90.

 do ipol = 1, 3
 do na = 1, nat
zstareu (ipol, ipol, na) = zstareu (ipol, ipol, na) + zv (ityp ( na) )
 enddo
  enddo

The zv values for Pb and S are 14 and 6 given in the PSP. If we subtract zv 
from the Born charges, we get the term due to polarization: -9.878 and -10.168. 
These values seem too large because of the argument below.

To estimate the polarization term, I reduce the alat by 1% and relax the atoms. 
This shifts the atoms from the unstrained position. I calculate the Bader 
charges for the unstrained and the strained cases. The change in the Bader 
charge is related to the atomic displacement. I have also tried keeping alat 
fixed and moving the atoms by 1%.

For unstrained PbS, the Bader charges are 12.998 and 7.001. 
For the strained PbS, they are 13.004 and 6.995.

So a ~1% change in atomic positions results in a +/-0.006 change in Bader 
charge. From this calculation, I expect the contribution from polarization to 
be u(dZ/du), where u is interatomic distance, which amount to +0.6 for Pb and 
-0.6 for S.

The contribution from polarization I get (0.6 and -0.6) are quite different 
from the those of the PHONON code (-9.878 and -10.168). I am assuming that the 
code is correct and my logic is flawed. I would appreciate any thoughts you may 
have on this discrepancy.

Thank you,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada
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[QE-users] Unit of velocities in Wannier90

[Vahid Askarpour]

Dear QE Community,

In the postw90 folder, in file Boltzmann.F90, it says,

 \param deleig_karray with the band derivatives at the given k point
   (in eV * angstrom / (2pi) as internally given by 
the code)

So deleig_k is the electron velocity at a given k-point. When we set 

geninterp=.true.
geninterp_alsofirstder=.true.

The postw90 output includes k-point coordinates (with units), energies (with 
units) and velocities (no units). Am I correct in assuming that these 
velocities are in eV*angstrom/(2pi)?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada
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Re: [QE-users] vc-relax crashes

[Vahid Askarpour]

May be you are using an older version of QE in which cell_dofree=‘ibrav’ was 
not implemented?

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada

On Mar 15, 2020, at 6:06 AM, Fariba Islam 
mailto:ezq...@gmail.com>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Hello,
I am following a tutorial and the following code was given there-
  &control
calculation = 'vc-relax'
prefix = 'Si_exc2'
outdir = './tmp/'
pseudo_dir = '../pseudo/'
etot_conv_thr = 1e-5
forc_conv_thr = 1e-4
/
&system
ibrav=2, celldm(1) =14,
nat=2, ntyp=1,
ecutwfc=30
/
&electrons
conv_thr=1e-7
/
&ions
/
&cell
cell_dofree='ibrav'
/
ATOMIC_SPECIES
 Si  28.0855  Si.pbe-n-rrkjus_psl.1.0.0.UPF



ATOMIC_POSITIONS (alat)
 Si 0.00 0.00 0.00 0 0 0
 Si 0.25 0.25 0.25 0 0 0
K_POINTS (automatic)
  4 4 4 0 0 0

I get the following error in CRASH-

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Re: [QE-users] Band structure with hybrid functionals

[Vahid Askarpour]

Dear Dominik,

I went back to my old files since I did the HSE band structure a couple of 
years ago. You are correct that the procedure works for nqx’s =1.  For higher 
nqx values, I used the wannier code along with the open_grid.x code.

Cheers,
Vahid

On Oct 28, 2019, at 6:19 AM, Dominik Gresch 
mailto:gres...@gmx.ch>> wrote:

Dear Vahid,

Thank you for your help. Unfortunately this produces the same error, unless the 
q-grid is set to one -- in which case the results may not be converged. Did you 
have to choose the band-structure point in any particular way to match with the 
k-grid?

Best regards,
Dominik

Gesendet: Samstag, 26. Oktober 2019 um 23:33 Uhr
Von: "Vahid Askarpour" mailto:vh261...@dal.ca>>
An: "Quantum ESPRESSO users Forum" 
mailto:users@lists.quantum-espresso.org>>
Betreff: Re: [QE-users] Band structure with hybrid functionals
To add to my earlier post, and not having seen your input file, it is possible 
that you set a q-grid (nqx’s) that is not an integer multiplier of the k-grid. 
So if the k-grid is 8x8x8 and the q-grid is 6x6x6 or 3x3x3, the calculation 
will crash. A q-grid of 2x2x2 or 4x4x4 would work.

Vahid

On Oct 26, 2019, at 6:34 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

I have calculated HSE band structure using the method you described. The only 
difference is that for the band-structure k-points, I used a weight of 0.000001 
instead of zero.

Cheers,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Oct 26, 2019, at 6:21 PM, Dominik Gresch 
mailto:gres...@gmx.ch>> wrote:

Dear QE users,

I am trying to calculate the band structure of a material with hybrid 
functionals. Since it is not possible to perform an NSCF run in that case, the 
desired k-points should be included in the SCF calculation. Since increasing 
the k-point mesh as a whole is rather expensive, I tried explicitly setting the 
list of k-points (in "crystal" mode), and then appending the desired k-points 
for the band structure as points with zero weight [0].

However, when trying this trick, I am faced with the following error:
%%
Error in routine exx_grid_init (117994):
k + q is not an S*k
%%

My questions are as follows:
- does anyone have experience in computing the band structure with hybrids, and 
if so, is this the right approach?
- what is the nature of this error, and is there some work-around?

Thank you and best regards,
Dominik Gresch
--
Microsoft Research

[0] I am familiar with using this technique from experience using VASP 
(described here: https://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure)
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Re: [QE-users] Band structure with hybrid functionals

[Vahid Askarpour]

To add to my earlier post, and not having seen your input file, it is possible 
that you set a q-grid (nqx’s) that is not an integer multiplier of the k-grid. 
So if the k-grid is 8x8x8 and the q-grid is 6x6x6 or 3x3x3, the calculation 
will crash. A q-grid of 2x2x2 or 4x4x4 would work.

Vahid

On Oct 26, 2019, at 6:34 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

I have calculated HSE band structure using the method you described. The only 
difference is that for the band-structure k-points, I used a weight of 0.01 
instead of zero.

Cheers,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Oct 26, 2019, at 6:21 PM, Dominik Gresch 
mailto:gres...@gmx.ch>> wrote:

Dear QE users,

I am trying to calculate the band structure of a material with hybrid 
functionals. Since it is not possible to perform an NSCF run in that case, the 
desired k-points should be included in the SCF calculation. Since increasing 
the k-point mesh as a whole is rather expensive, I tried explicitly setting the 
list of k-points (in "crystal" mode), and then appending the desired k-points 
for the band structure as points with zero weight [0].

However, when trying this trick, I am faced with the following error:
%%
Error in routine exx_grid_init (117994):
k + q is not an S*k
%%

My questions are as follows:
- does anyone have experience in computing the band structure with hybrids, and 
if so, is this the right approach?
- what is the nature of this error, and is there some work-around?

Thank you and best regards,
Dominik Gresch
--
Microsoft Research

[0] I am familiar with using this technique from experience using VASP 
(described here: https://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure)
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Re: [QE-users] Band structure with hybrid functionals

[Vahid Askarpour]

I have calculated HSE band structure using the method you described. The only 
difference is that for the band-structure k-points, I used a weight of 0.01 
instead of zero.

Cheers,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Oct 26, 2019, at 6:21 PM, Dominik Gresch 
mailto:gres...@gmx.ch>> wrote:

Dear QE users,

I am trying to calculate the band structure of a material with hybrid 
functionals. Since it is not possible to perform an NSCF run in that case, the 
desired k-points should be included in the SCF calculation. Since increasing 
the k-point mesh as a whole is rather expensive, I tried explicitly setting the 
list of k-points (in "crystal" mode), and then appending the desired k-points 
for the band structure as points with zero weight [0].

However, when trying this trick, I am faced with the following error:
%%
Error in routine exx_grid_init (117994):
k + q is not an S*k
%%

My questions are as follows:
- does anyone have experience in computing the band structure with hybrids, and 
if so, is this the right approach?
- what is the nature of this error, and is there some work-around?

Thank you and best regards,
Dominik Gresch
--
Microsoft Research

[0] I am familiar with using this technique from experience using VASP 
(described here: https://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure)
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Re: [QE-users] Tetragolan atomic position

[Vahid Askarpour]

Why not google it? I did and here is a link:

https://onlinelibrary.wiley.com/doi/pdf/10.1002/zaac.19683610110

Cheers,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Apr 13, 2019, at 4:11 PM, Mahsa Soltani 
mailto:mahsasolta...@yahoo.com>> wrote:

Hi
What is tetragonal atomic position??
I am searching for tetragonal FeS atomic position
Could you help me please?
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Re: [QE-users] thermo_pw crashes with "can't open a connected unit"

[Vahid Askarpour]

The error seems to be related to lack of bfgs ionic convergence for each 
structure. Several structures goes through 20 steps but do not reach 
convergence. The remaining ones go through 0 bfgs steps. 

So I changed nstep in set_thermo_work_todo.f90 from 20 to 50. Now what happens 
is that the first structure converges in say 25 steps but the other structures  
go through 0 bfgs steps. They remain unconverged even though for each of them 
nstep should be 50. 

Vahid



> On Dec 13, 2018, at 3:23 PM, Vahid Askarpour  wrote:
> 
> This is likely a bug in the thermo_pw code. When I use “lmurn=.TRUE.”, the 
> error disappears. 
> 
> However, I need to use “lmurn=.FALSE.” in order to change all the 
> orthorhombic lattice constants and not just celldm(1).
> 
> Vahid
> 
>> On Dec 13, 2018, at 11:19 AM, Vahid Askarpour  wrote:
>> 
>> Dear QE community,
>> 
>> I have installed the latest thermo_pw along with qe-6.3 and successfully 
>> finished QHA calculation for example09 for Si. However, when I redo the 
>> calculations for SnSe, I get the following error just as the code starts to 
>> do phonon calculations:
>> 
>> Electric Fields Calculation
>> 
>> iter #   1 total cpu time :11.2 secs   av.it.:   5.8
>> thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  2.283E+10
>> 
>> %%
>>Error in routine seqopn (99):
>>can't open a connected unit
>> %%
>> 
>> The error originates from line 430 of io_files.f90 in the Modules folder:
>> 
>> inquire (unit = unit, opened = opnd)
>> if (opnd) call errore ('seqopn', "can't open a connected unit",  abs (unit) )
>> 
>> It appears that a file should not be open but it is.
>> 
>> My input thermo_pw file is:
>> 
>> &INPUT_THERMO
>> what='mur_lc_t',
>> lmurn=.FALSE.
>> deltat=3.
>> /
>> 
>> My other two QE input files are:
>> 
>> &control
>>  calculation = 'scf'
>>  prefix='tinsel',
>>  pseudo_dir = './',
>>  outdir='./tempdir'
>> /
>> &system
>>   ibrav=8,
>>   nat=8 , ntyp= 2, 
>>   celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894
>>   ecutwfc = 90, 
>>   occupations='fixed'
>>   nr1=150,nr2=50,nr3=50
>> /
>> &electrons
>>   conv_thr =  1.0d-5
>> /
>> ATOMIC_SPECIES
>> Sn 118.71 Sn.pz-hgh.UPF
>> Se 78.96  Se.pz-hgh.UPF
>> ATOMIC_POSITIONS (crystal)
>> Sn   0.882841736   0.25000   0.602195343
>> Sn   0.617158264   0.75000   0.102195343
>> Sn   0.382841736   0.25000   0.897804657
>> Sn   0.117158264   0.75000   0.397804657
>> Se   0.142813748   0.25000   0.976427467
>> Se   0.357186252   0.75000   0.476427467
>> Se   0.642813748   0.25000   0.523572533
>> Se   0.857186252   0.75000   0.023572533
>> K_POINTS AUTOMATIC
>> 2 2 2 0 0 0
>> 
>> And for phonon calculation:
>> 
>> SnSe-Pnma
>> &inputph
>> tr2_ph=1.0d-9,
>> prefix='tinsel',
>> fildyn='SnSe.dyn.xml',
>> ldisp=.TRUE.
>> epsil=.TRUE.
>> nq1=2, nq2=2, nq3=2,
>> /
>> 
>> If you have encountered this error (or possible bug), I would really 
>> appreciate hearing from you. 
>> 
>> Thank you,
>> 
>> Vahid
>> 
>> Vahid Askarpour
>> Department of Physics and Atmospheric Science
>> Dalhousie University,
>> Halifax, NS, Canada
>> 
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Re: [QE-users] thermo_pw crashes with "can't open a connected unit"

[Vahid Askarpour]

This is likely a bug in the thermo_pw code. When I use “lmurn=.TRUE.”, the 
error disappears. 

However, I need to use “lmurn=.FALSE.” in order to change all the orthorhombic 
lattice constants and not just celldm(1).

Vahid

> On Dec 13, 2018, at 11:19 AM, Vahid Askarpour  wrote:
> 
> Dear QE community,
> 
> I have installed the latest thermo_pw along with qe-6.3 and successfully 
> finished QHA calculation for example09 for Si. However, when I redo the 
> calculations for SnSe, I get the following error just as the code starts to 
> do phonon calculations:
> 
> Electric Fields Calculation
> 
>  iter #   1 total cpu time :11.2 secs   av.it.:   5.8
>  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  2.283E+10
> 
> %%
> Error in routine seqopn (99):
> can't open a connected unit
> %%
> 
> The error originates from line 430 of io_files.f90 in the Modules folder:
> 
>  inquire (unit = unit, opened = opnd)
>  if (opnd) call errore ('seqopn', "can't open a connected unit",  abs (unit) )
> 
> It appears that a file should not be open but it is.
> 
> My input thermo_pw file is:
> 
> &INPUT_THERMO
>  what='mur_lc_t',
>  lmurn=.FALSE.
>  deltat=3.
> /
> 
> My other two QE input files are:
> 
> &control
>   calculation = 'scf'
>   prefix='tinsel',
>   pseudo_dir = './',
>   outdir='./tempdir'
> /
> &system
>ibrav=8,
>nat=8 , ntyp= 2, 
>celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894
>ecutwfc = 90, 
>occupations='fixed'
>nr1=150,nr2=50,nr3=50
> /
> &electrons
>conv_thr =  1.0d-5
> /
> ATOMIC_SPECIES
> Sn 118.71 Sn.pz-hgh.UPF
> Se 78.96  Se.pz-hgh.UPF
> ATOMIC_POSITIONS (crystal)
> Sn   0.882841736   0.25000   0.602195343
> Sn   0.617158264   0.75000   0.102195343
> Sn   0.382841736   0.25000   0.897804657
> Sn   0.117158264   0.75000   0.397804657
> Se   0.142813748   0.25000   0.976427467
> Se   0.357186252   0.75000   0.476427467
> Se   0.642813748   0.25000   0.523572533
> Se   0.857186252   0.75000   0.023572533
> K_POINTS AUTOMATIC
> 2 2 2 0 0 0
> 
> And for phonon calculation:
> 
> SnSe-Pnma
> &inputph
>  tr2_ph=1.0d-9,
>  prefix='tinsel',
>  fildyn='SnSe.dyn.xml',
>  ldisp=.TRUE.
>  epsil=.TRUE.
>  nq1=2, nq2=2, nq3=2,
> /
> 
> If you have encountered this error (or possible bug), I would really 
> appreciate hearing from you. 
> 
> Thank you,
> 
> Vahid
> 
> Vahid Askarpour
> Department of Physics and Atmospheric Science
> Dalhousie University,
> Halifax, NS, Canada
> 
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[QE-users] thermo_pw crashes with "can't open a connected unit"

[Vahid Askarpour]

Dear QE community,

I have installed the latest thermo_pw along with qe-6.3 and successfully 
finished QHA calculation for example09 for Si. However, when I redo the 
calculations for SnSe, I get the following error just as the code starts to do 
phonon calculations:

 Electric Fields Calculation

  iter #   1 total cpu time :11.2 secs   av.it.:   5.8
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  2.283E+10

 %%
 Error in routine seqopn (99):
 can't open a connected unit
 %%

The error originates from line 430 of io_files.f90 in the Modules folder:

  inquire (unit = unit, opened = opnd)
  if (opnd) call errore ('seqopn', "can't open a connected unit",  abs (unit) )

It appears that a file should not be open but it is.

My input thermo_pw file is:

 &INPUT_THERMO
  what='mur_lc_t',
  lmurn=.FALSE.
  deltat=3.
 /

My other two QE input files are:

 &control
   calculation = 'scf'
   prefix='tinsel',
   pseudo_dir = './',
   outdir='./tempdir'
 /
 &system
ibrav=8,
nat=8 , ntyp= 2, 
celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894
ecutwfc = 90, 
occupations='fixed'
nr1=150,nr2=50,nr3=50
 /
 &electrons
conv_thr =  1.0d-5
 /
ATOMIC_SPECIES
Sn 118.71 Sn.pz-hgh.UPF
Se 78.96  Se.pz-hgh.UPF
ATOMIC_POSITIONS (crystal)
Sn   0.882841736   0.25000   0.602195343
Sn   0.617158264   0.75000   0.102195343
Sn   0.382841736   0.25000   0.897804657
Sn   0.117158264   0.75000   0.397804657
Se   0.142813748   0.25000   0.976427467
Se   0.357186252   0.75000   0.476427467
Se   0.642813748   0.25000   0.523572533
Se   0.857186252   0.75000   0.023572533
K_POINTS AUTOMATIC
2 2 2 0 0 0

And for phonon calculation:

SnSe-Pnma
 &inputph
  tr2_ph=1.0d-9,
  prefix='tinsel',
  fildyn='SnSe.dyn.xml',
  ldisp=.TRUE.
  epsil=.TRUE.
  nq1=2, nq2=2, nq3=2,
/

If you have encountered this error (or possible bug), I would really appreciate 
hearing from you. 

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

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[QE-users] Hard PSP for Bismuth with ld1.x

[Vahid Askarpour]

Dear QE Users,

Following Dr. Giannozzi’s notes on PSP generation, I have successfully 
generated an LDA norm-conserving fully-relativistic Bi PSP (with 5d10 states) 
using the following input:

&input
   title='Bi',
   zed=83.,
   rel=2
   config='[Xe] 4f14  6s2 6p3 5d10',
   rlderiv=2.9, eminld=-2.0, emaxld=2.0, deld=0.01, nld=3,
   iswitch=3,
 /
 &inputp
   lpaw=.false.,
   pseudotype=2,
   file_pseudopw='Bi.UPF',
   author='Vahid',
   lloc=0
   nlcc=.true.
   tm=.true.
/
3
5D  3  2 10.00  0.00  1.60  1.60  0.0
6P  2  1   3.00  0.00  2.40  2.40  0.0
6S  1  0   2.00  0.00  2.00  2.00  0.0

I would like to make this PSP harder by adding the 5S and 5P electrons. I use 
the following input:

&input
   title='Bi',
   zed=83.,
   rel=2
   config='[Xe] 4f14  6s2 6p3 5d10',
   rlderiv=2.9, eminld=-2.0, emaxld=2.0, deld=0.01, nld=5,
   iswitch=3,
 /
 &inputp
   lpaw=.false.,
   pseudotype=2,
   file_pseudopw='Bi.UPF',
   author='Vahid',
   lloc=1,
   nlcc=.true.,
   tm=.true.
/
5
5D  3  2 10.00  0.00  1.20  1.20  0.0
5S  1  0   2.00  0.00  1.20  1.20  0.0
5P  2  1   6.00  0.00  1.20  1.20  0.0
6S  1  0   2.00  0.00  1.20  1.20  0.0
6P  2  1   3.00  0.00  1.20  1.20  0.0

I get 

   Warning: n=3, l=2 expected 0 nodes, found 1
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)


 %%
 Error in routine run_pseudo (1):
 Errors in PS-KS equation
 %%

I have tried the followings:

1. Change the rcut values
2. Use lloc=0 with 6S at the bottom of the list
3. Use lloc=-1 with various rcloc values

I always get the above error except when I set lloc=-1 and rcloc=1.2. In this 
case I get good matching of AE and PS energies but the bmat is NaN and so are 
many of the printed energies.

 n l  j  nl e AE (Ry)   e PS (Ry)De AE-PS (Ry) 
 3 2 1.5 5D   1( 4.00)   -2.06502   -2.065020.0
 3 2 2.5 5D   1( 6.00)   -1.84371   -1.843710.0
 1 0 0.5 5S   1( 2.00) -11.51388  -11.513880.0
 2 1 0.5 5P   1( 2.00)   -8.32746   -8.327460.0
 2 1 1.5 5P   1( 4.00)   -6.49718   -6.497180.0
 1 0 0.5 6S   1( 2.00)   -1.03807   -1.038070.0
 2 1 0.5 6P   1( 2.00)   -0.42584   -0.425840.0
 2 1 1.5 6P   1( 1.00)   -0.28668   -0.286680.0

 eps = NaN  iter =201

 Etot =  -43140.018305 Ry,  -21570.009153 Ha, -586949.798927 eV
 Etotps =  NaN Ry,NaN Ha,NaN eV

 Ekin =NaN Ry,NaN Ha,NaN eV
 Encl =NaN Ry,NaN Ha,NaN eV
 Ehrt =   0.00 Ry,   0.00 Ha,   0.00 eV
 Ecxc =-145.329988 Ry, -72.664994 Ha,   -1977.315048 eV
 (Ecc =-145.329988 Ry, -72.664994 Ha,   -1977.315048 eV)

Does anyone have any suggestions for what I might be missing from the above 
procedure?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [QE-users] Possibility of jump in k-points in Bandstructure

[Vahid Askarpour]

Looking at the plotband.f90 code, jumps are allowed:

 IF (dxmod > 5*dxmod_save) THEN
!
!   A big jump in dxmod is a sign that the point k(:,n) and k(:,n-1)
!   are quite distant and belong to two different lines. We put them on
!   the same point in the graph 
!
kx(n)=kx(n-1)

Cheers,

Vahid
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[QE-users] Possibility of jump in k-points in Bandstructure

[Vahid Askarpour]

Dear QE community,

I tried to reproduce the Si phonon dispersion along G-K-X-G-L in the following 
link (http://exciting-code.org/lithium-phonon-and-thermal-properties-si). The 
point K appears to be actually U. It seems that their code allows to jump from 
U to K (which are energetically equivalent but are distant from each other) 
without any gap along the k-path (x-axis). So they go from G to U, then jump 
from U to K and continue up to L.

Is it possible in QE to jump from one high symmetry point U to another point K 
and not have a k-distance gap along the x-axis when calculating band structure?

Thanks,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] Plotting phonon dispersion

[Vahid Askarpour]

1. You could use the ibrav=0 results. In the matdyn.in, do not use

gG 50
 X 50
 M 50
 gG 8

Instead, explicitly give the coordinates of each high-symmetry point in 
cartesian.

2. Four days sounds like a long time unless you are running on few nodes. If a 
run takes several days, you can break it up into several parts using start_q 
and last_q.

3. I am not sure if specifying the high-symmetry points by just using their 
labels in matdyn.in will work for ibrav=6. It might.

Cheers,

Vahid



> On Feb 19, 2018, at 2:27 PM, elch...@auth.gr wrote:
> 
> 
> Ok, I am confused again.
> 
> I used ibrav=0 in the scf run that eventually gave me the error in matdyn.x.
> 
> I am running it again. This time I've used,
> 
> -
> ibrav = 6,
> celldm(1) = [..]
> celldm(3) = [..]
> --
> 
> in the scf. It's good to know if this is more possible to work as ph.x  
> takes about 4 days.
> 
> 
> Eleni
> 
> 
> 
> Quoting Lorenzo Paulatto :
> 
>> On 02/19/2018 03:14 PM, Saif Ullah wrote:
>>> Dear Eleni,
>>> 
>>> Did you use ibrav=0? If so, then you need to use q_in_band_form=.false.
>>> q_in_cryst_coord=.true.
>>> 
>> Neither of these two bits of advice is correct:
>> 
>> 1. q_in_band_form can be used with ibrav=0 as usual, and works just as
>> well as long as you specify the point coordinates
>> 2. there is no specific reason to use crystal coordinates with ibrav=0,
>> you can, as usual, but by no mean you "need to"
>> 
>> 
>> kind regards
>> 
>> 
>> --
>> Lorenzo Paulatto - Paris
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> 
> 
> 
> -- 
> Dr. Eleni Chatzikyriakou
> Computational Physics lab
> Aristotle University of Thessaloniki
> elch...@auth.gr - tel:+30 2310 998109
> 
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Re: [Pw_forum] Plotting phonon dispersion

[Vahid Askarpour]

a) If you skip amass, I think the codes use the mass in the previous runs. 

b) Did you use ibrav=0 in the scf run? The high-symmetry points you defined are 
for ibrav=2. Otherwise, just specify the coordinates explicitly.

Cheers,

Vahid

> On Feb 19, 2018, at 9:29 AM, elch...@auth.gr wrote:
> 
> 
> Thank you Vahid Askarpour.
> 
> I have two questions:
> 
> a) Is there a problem if I don't specify amass?
> 
> b) I have already done this procedure using the following files:
> 
> ph.x:
> 
> &inputph
>   prefix   = 'Si',
>   epsil= .false.,
>   fildyn   = 'diam.dyn',
>   ldisp= .true.
>   fildvscf = 'dvscf'
>   nq1=6,
>   nq2=6,
>   nq3=1,
>   tr2_ph   =  1.0d-12,
>   recover = .true.
>  /
> 
> This run ok
> 
> q2r.in:
> 
>  &input
>   fildyn='diam.dyn',
>   flfrc='Si.rc'
>  /
> 
> This run ok
> 
> matdyn.in:
> 
>  &input
> flfrc='Si.rc',
> flfrq='Si.freq',
> q_in_band_form=.true.
>  /
>  4
>  gG 50
>   X 50
>   M 50
>   gG 8
> 
> And I got the following error:
> 
> 
> %%
>  Error in routine find_bz_type (1):
>  Wrong ibrav
> 
> %%%%%%
> 
> Is it possible that this is because I messed up the names of the  
> files, or do I need to include explicitly the coordinates of the high  
> symmetry points?
> 
> 
> Regards
> 
> Eleni
> 
> 
> 
> 
> Quoting Vahid Askarpour :
> 
>> Once you get all the .dyn files from the ph.x run, use the following  
>> input to q2r.x to get the force constants:
>> 
>> &input
>>   fildyn=’Si.dyn', zasr='simple', flfrc=’Si.ifc2’
>> /
>> 
>> Then use the following input to matdyn.x:
>> 
>> &input
>>asr='simple',  amass(1)= 28.0855
>>flfrc=’Si.ifc2', flfrq=’Si.freq', q_in_band_form=.true.
>> /
>> 6  ! number of high-symmetry points
>> 0.0 0.0 0.0 200
>> 0.0 0.0 1.0 200
>> etc.
>> 
>> The coordinates of the high symmetry points should be in cartesian  
>> coordinates. 200 points will be calculated for each segment. The  
>> phonon dispersion is in the .gp output file.
>> 
>> Cheers,
>> 
>> Vahid
>> 
>> Vahid Askarpour
>> Department of Physics and Atmospheric Science
>> Dalhousie University,
>> Halifax, NS, Canada
>> 
>>> On Feb 19, 2018, at 4:54 AM, elch...@auth.gr wrote:
>>> 
>>> Hello all,
>>> 
>>> I am using ph.x to get the phonon frequencies and dynamical matrices
>>> for an epw.x calculation, however, I would like to plot my phonon
>>> dispersions from the ph.x calculation for far, as for example is shown
>>> in
>>> 
>>> http://epw.org.uk/Documentation/B-dopedDiamond
>>> 
>>> I am lost as to how I can do that. My ph.x file is as follows,
>>> 
>>> &inputph
>>>  prefix   = 'Si',
>>>  epsil= .false.,
>>>  fildyn   = 'diam.dyn',
>>>  ldisp= .true.
>>>  fildvscf = 'dvscf'
>>>  nq1=6,
>>>  nq2=6,
>>>  nq3=1,
>>>  tr2_ph   =  1.0d-12,
>>>  recover = .true.
>>> /
>>> 
>>> Do I need to use q2r.x and matdyn.x to the files for plotting?
>>> 
>>> 
>>> Thank you
>>> 
>>> 
>>> 
>>> --
>>> Dr. Eleni Chatzikyriakou
>>> Computational Physics lab
>>> Aristotle University of Thessaloniki
>>> elch...@auth.gr - tel:+30 2310 998109
>>> 
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>> 
>> 
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> 
> 
> 
> -- 
> Dr. Eleni Chatzikyriakou
> Computational Physics lab
> Aristotle University of Thessaloniki
> elch...@auth.gr - tel:+30 2310 998109
> 
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Re: [Pw_forum] Plotting phonon dispersion

[Vahid Askarpour]

Once you get all the .dyn files from the ph.x run, use the following input to 
q2r.x to get the force constants:

 &input
   fildyn=’Si.dyn', zasr='simple', flfrc=’Si.ifc2’
/

Then use the following input to matdyn.x:

&input
asr='simple',  amass(1)= 28.0855
flfrc=’Si.ifc2', flfrq=’Si.freq', q_in_band_form=.true.
/
6  ! number of high-symmetry points
0.0 0.0 0.0 200  
0.0 0.0 1.0 200  
etc.

The coordinates of the high symmetry points should be in cartesian coordinates. 
200 points will be calculated for each segment. The phonon dispersion is in the 
.gp output file.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

> On Feb 19, 2018, at 4:54 AM, elch...@auth.gr wrote:
> 
> Hello all,
> 
> I am using ph.x to get the phonon frequencies and dynamical matrices  
> for an epw.x calculation, however, I would like to plot my phonon  
> dispersions from the ph.x calculation for far, as for example is shown  
> in
> 
> http://epw.org.uk/Documentation/B-dopedDiamond
> 
> I am lost as to how I can do that. My ph.x file is as follows,
> 
> &inputph
>   prefix   = 'Si',
>   epsil= .false.,
>   fildyn   = 'diam.dyn',
>   ldisp= .true.
>   fildvscf = 'dvscf'
>   nq1=6,
>   nq2=6,
>   nq3=1,
>   tr2_ph   =  1.0d-12,
>   recover = .true.
>  /
> 
> Do I need to use q2r.x and matdyn.x to the files for plotting?
> 
> 
> Thank you
> 
> 
> 
> -- 
> Dr. Eleni Chatzikyriakou
> Computational Physics lab
> Aristotle University of Thessaloniki
> elch...@auth.gr - tel:+30 2310 998109
> 
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Re: [Pw_forum] Error in DOS calculation ( Spin orbit coupling )

[Vahid Askarpour]

You have a total of 36 electrons. This means 18 bands without spin-orbit and 36 
bands with spin-orbit for the valence states. Your scf.out specifies 44 bands 
in total (36 valence+8 conduction). But in your nscf.in, you specify nbnd=26.

Maybe if you leave out the nbnd in nscf.in, you avoid this problem.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

> On Jan 28, 2018, at 2:50 PM, Anik Mondol  wrote:
> 
> 


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Re: [Pw_forum] Relativistic NC-PP's for uranium

[Vahid Askarpour]

You can download rel-pz.0.3.1.tgz from the following website: 

http://theossrv1.epfl.ch/Main/Pseudopotentials

The file includes norm-conserving LDA full-relativistic pseudopotentials. Also 
available are the PBE counterparts.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

> On Jan 26, 2018, at 10:10 AM, Malte Sachs  
> wrote:
> 
> Dear all,
> 
> I want to calculate the orbital-magnetization of uranium compounds. Thus, I 
> am looking for full-relativistic norm-conserving pseudopotentials for 
> uranium. Up to know, I could not manage it to build my own ones. I also 
> didn't find any relativistic uranium pseudos in the databases listed at the 
> quantum espresso homepage. Does anyone have an idea, where I can look to find 
> such kind of pp's?
> 
> Thank you and best regards,
> 
> Malte Sachs
> 
> -- 
> Malte Sachs
> Anorganische Chemie, Fluorchemie
> Philipps-Universität Marburg
> Hans-Meerwein-Straße 4
> 35032 Marburg (Paketpost: 35043 Marburg)
> Tel.: +49 (0)6421 28 - 25 68 0
> http://www.uni-marburg.de/fb15/ag-kraus/
> 
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Re: [Pw_forum] ibrav = 13 monoclinic-base-centered unique axis

[Vahid Askarpour]

Hi,

Shouldn’t this be uniqueb instead of unique_b?

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Jan 25, 2018, at 3:17 PM, José C. Conesa 
mailto:jccon...@icp.csic.es>> wrote:


Hi,

This did not work. By including:



&system
ibrav=-13
space_group=12
unique_b=.true.
A=14.3100,B=6.3383,C=10.1995,cosAC=-0.70644
.

this error appeared:

 %%
 Error in routine  read_namelists (19):
  bad line in namelist &system: "unique_b=.true." (error could be in 
the previous line)
 %%


What should be done?
Thanks in advance,
JC Conesa

El 25/01/2018 a las 18:12, Paolo Giannozzi escribió:
On Thu, Jan 25, 2018 at 5:34 PM, José Carlos Conesa 
mailto:jccon...@icp.csic.es>> wrote:

  Input ibrav not compatible with space group number

You may need to specify "unique_b=.true."

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

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Re: [Pw_forum] Does number of atoms change after optimization

[Vahid Askarpour]

The FINDSYM code (http://stokes.byu.edu/iso/findsym.php) takes as input a 
primitive or conventional cell and returns the primitive cell along with the 
Wyckoff positions, space group and primitive lattice vectors/constants.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Dec 25, 2017, at 3:58 PM, Manu Hegde 
mailto:mhe...@uwaterloo.ca>> wrote:

if you know the Wyckoff position you can estimate  it.

On Dec 25, 2017 1:56 PM, "Madhurya Chandel" 
mailto:madhurya.sv...@gmail.com>> wrote:
Thank you so much for your reply.

In input script you have given conventional unit cell, and all calculation  in 
pwscf are done via primitive unit cell.
How i can get to know that calculation are done via primitive unit cell? What 
are the points in input file that can change unit cell from conventional to 
primitive?
Can you please explain little bit more?

So in output script it is primitive unit cell. No need to worry, just take 
optimised coordinate from out put...

Thank you.

On 25-Dec-2017 6:05 PM, "Madhurya Chandel" 
mailto:madhurya.sv...@gmail.com>> wrote:
Dear QE users

I have a small doubt that after optimization (relax) does the number of atoms 
change?
Because in my case its happening.

For the reference, I am attaching the input and output images of the unit cell.

Please have a look.



With regards
Madhurya Chandel
Research Scholar
Department of Chemistry
BITS PILANI, GOA campus
+91-7507546773

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Research Scholar
Department of Chemistry
BITS PILANI, GOA campus
+91-7507546773

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Re: [Pw_forum] Reg: Plotting of phonon dispersion with inclusion of spin-orbit coupling

[Vahid Askarpour]

For GaN, I use the following q2r.in:

&input
fildyn=“peace.xml"
zasr='simple',
flfrc='gan.fc'
/
6 6 6
28
gan.dyn1
gan.dyn2
gan.dyn3
….
….
Gan.dyn28

You may replace peace with your favourite word.

For matdyn.in, I use the following matdyn.in:

 &input
asr='simple',amass(1) = 69.723, amass(2) = 14.007,
flfrc='gan.fc.xml', flfrq='gan.crystal.freq', q_in_cryst_coord=.true.
 /
 231
 0.000   0.000   0.000   0
 0.017  -0.008   0.000   0
 0.033  -0.017   0.000   0
 0.050  -0.025   0.000   0
 0.067  -0.033   0.000   0
 …..
 …..

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Dec 25, 2017, at 3:40 AM, pachineela rambabu 
mailto:rams@gmail.com>> wrote:

Dear Forum,
 I have run a ph.x calculation for phonon dispersion including 
spin-orbit coupling using 4x4x4 grid with qe5.4.0. version. At the end of the 
calculation, I got dyn files in case.dyn.xml format instead of case.dyn. Here I 
am unable to use this case.dyn.xml for further running q2r.x and matdyn.x to 
obtain case.fc and case.freq. Please help me in this regard.

thanks in advance,
--
P. Rambabu
PhD Scholor
Department of Physics, IIT Hyderabad,
Kandi, SangaReddy, Telangana, India.
Mobile: 9074508220.
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Re: [Pw_forum] SOC pseudopotential

[Vahid Askarpour]

Dear Eliya,

Those PSPs were generated with the atomic code. I guess users can generate 
their own PSPs if they are not readily available.

Cheers,

Vahid

On Dec 5, 2017, at 3:06 AM, Eliya Asmani 
mailto:eliya6...@gmail.com>> wrote:

Dear Vahid,

Thank you for your guidance.
It contains NC fully relativistic PS for many elements. But unfortunately It 
doesn't have any thing for W.

Best
Eliya

On Tue, Dec 5, 2017 at 2:14 AM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:
The website http://theossrv1.epfl.ch/Main/Pseudopotentials has untested NC 
fully relativistic PSP for both PBE and PZ (LDA). They are in the files 
rel-pbe.0.3.1.tgz and rel-pz.0.3.1.tgz.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Dec 4, 2017, at 12:00 PM, Eliya Asmani 
mailto:eliya6...@gmail.com>> wrote:

Dear Lorenzo,

Thanks for your reply.

I want to calculate optical properties and it is important to consider SOC in 
our calculations. About norm-conserving pseudopotential, I'm not sure. But I 
don't know why it is usually used the norm-conserving PP. I would be glad 
somebody can give me  any suggestions about it.

Best,
Eliya Asmani,

School of Physics, Institute for Research in Fundamental Sciences (IPM)
 Tehran, Iran



On Mon, Dec 4, 2017 at 11:21 AM, Lorenzo Paulatto 
mailto:paul...@gmail.com>> wrote:
> I would like to perform calculations for w and Te with SOC effect. I
> could not find full relativistic _normconserving_ pseudopotential for
> them.

Hello,
why do you need this specific combination? I cannot think of any code
that can do SOC but not US. Mostly thanks to Andrea Dal Corso being the
main author of both.

That said, I was able to re-generate some of the SG15-ONCV
pseudopotentials (which are norm-conserving) with the full-relativistic
version of the ONCV code, without too much hassle, just spending a day
reading the documentation and testing.

Disclaimer!
Please note that:
1. I am in no way related to the SG15 library or the ONCV code
2. I do not have time to support every code in the world.

Please do NOT ask ME for help on this subject, I won't provide any.

kind regards


> As I know in PSlibrary, we can make  just for  Ultrasoft and PAW
> pseudopotentials.
>
> Can someone quid me to find it?
>
> Eliya Asmani,
> Postdoctoral Researcher
> School of Physics, Institute for Research in Fundamental Sciences (IPM)
> Tehran, Iran
>
>
>
>
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Re: [Pw_forum] SOC pseudopotential

[Vahid Askarpour]

The website http://theossrv1.epfl.ch/Main/Pseudopotentials has untested NC 
fully relativistic PSP for both PBE and PZ (LDA). They are in the files 
rel-pbe.0.3.1.tgz and rel-pz.0.3.1.tgz.

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Dec 4, 2017, at 12:00 PM, Eliya Asmani 
mailto:eliya6...@gmail.com>> wrote:

Dear Lorenzo,

Thanks for your reply.

I want to calculate optical properties and it is important to consider SOC in 
our calculations. About norm-conserving pseudopotential, I'm not sure. But I 
don't know why it is usually used the norm-conserving PP. I would be glad 
somebody can give me  any suggestions about it.

Best,
Eliya Asmani,

School of Physics, Institute for Research in Fundamental Sciences (IPM)
 Tehran, Iran



On Mon, Dec 4, 2017 at 11:21 AM, Lorenzo Paulatto 
mailto:paul...@gmail.com>> wrote:
> I would like to perform calculations for w and Te with SOC effect. I
> could not find full relativistic _normconserving_ pseudopotential for
> them.

Hello,
why do you need this specific combination? I cannot think of any code
that can do SOC but not US. Mostly thanks to Andrea Dal Corso being the
main author of both.

That said, I was able to re-generate some of the SG15-ONCV
pseudopotentials (which are norm-conserving) with the full-relativistic
version of the ONCV code, without too much hassle, just spending a day
reading the documentation and testing.

Disclaimer!
Please note that:
1. I am in no way related to the SG15 library or the ONCV code
2. I do not have time to support every code in the world.

Please do NOT ask ME for help on this subject, I won't provide any.

kind regards


> As I know in PSlibrary, we can make  just for  Ultrasoft and PAW
> pseudopotentials.
>
> Can someone quid me to find it?
>
> Eliya Asmani,
> Postdoctoral Researcher
> School of Physics, Institute for Research in Fundamental Sciences (IPM)
> Tehran, Iran
>
>
>
>
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Re: [Pw_forum] dos.x : segmentation fault occurred

[Vahid Askarpour]

I think the input to dos.x (I call it dos.in) looks like this:

 &DOS
   outdir='./'
   prefix=‘graphene'
   fildos=‘graphene.dos',
   Emin=-10.0, Emax=16, DeltaE=0.002
/

You run dos.x after the nscf run. I think the nscf.in should contain the 
relaxed structure.

For the definition of Emin, Emax and DeltaE, see the online dos.x manual.


Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

On Nov 6, 2017, at 4:19 PM, B S Bhushan 
mailto:ecebhus...@gmail.com>> wrote:

Dear Experts,

I am trying to extract the DOS profiles for some graphene systems using 
Supercomputing facility.

First, I performed VC-relax and then NSCF (I have not manually updated the 
relaxed coordinates in the nscf input file, since nscf automatically reads them 
from previous scf run). Then I tried to execute dos.x, however I am getting 
segmentation fault error as shown below.

%%
 Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at 23:32:32

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL 
http://www.quantum-espresso.org<http://www.quantum-espresso.org/>",
 in publications or presentations arising from this work. More details at
 http://www.quantum-espresso.org/quote

 Parallel version (MPI), running on16 processors
 R & G space division:  proc/nbgrp/npool/nimage =  16

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1, nr2, nr3 values from input
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLineSource
dos.x  0073A4B1  qexml_module_mp_q3753  qexml.f90
dos.x  0055AD27  pw_restart_mp_rea2101  
pw_restart.f90
dos.x  005579E4  pw_restart_mp_pw_1057  
pw_restart.f90
dos.x  0040A828  read_xml_file_240  
read_file.f90
dos.x  00406331  MAIN__ 95  dos.f90
dos.x  0040621C  Unknown   Unknown  Unknown
libc.so.6  003FF541ECDD  Unknown   Unknown  Unknown
dos.x  00406119  Unknown   Unknown  Unknown
%%


I am not getting any error, if I run dos.x directly after vc-relax. However, If 
I run dos.x after NSCF the error appears.

The input script for vc-relax, nscf are attached with the mail here.

I thank you very much for your precious time and knowledge.


Sincerely,
B S Bhushan
Ph.D Scholar,
ABV-IIITM Gwalior, India.


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Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)

[Vahid Askarpour]

Dear Nam,

My understanding is that the trajectory as printed in VASP’s XDATCAR is folded 
or wrapped. As you can see in msd.f90,:

write(6,*) 'Name of unwrapped xyz file’

So the input file should be unwrapped. In other words, you have to first unwrap 
the coordinates in XDATCAR. Then you can use msd.f90.

To unwrap the coordinates, there are other codes on that website such as 
unwrap_PBC.f90.

Cheers,

Vahid


On Oct 30, 2017, at 9:25 PM, Nam Tran 
mailto:vnt...@uowmail.edu.au>> wrote:

Dear Vahid

I don't know whether VASP folds back atoms in their output or not. If they do 
then the msd.f90 you recommended is not accurate. Because the code simply 
calculate the distance between two position

dRx = Rx(j) - Rx0(j)
dRy = Ry(j) - Ry0(j)
dRz = Rz(j) - Rz0(j)
sum_msd = sum_msd + (dRx**2 + dRy**2 + dRz**2)

One thing is that I tried to create a .axsf file using cppx. And the atoms seem 
to be not folded back. Can someone confirm me that?

Best Regards,
Nam Tran



From: pw_forum-boun...@pwscf.org<mailto:pw_forum-boun...@pwscf.org> 
mailto:pw_forum-boun...@pwscf.org>> on behalf of 
Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Monday, October 30, 2017 11:00:01 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)

There is a collection of fortran codes (for VASP mainly but can easily be 
adapted) for processing simulation output including MSD calculation and the 
treatment of periodic images. They can be found at https://github.com/boates 
under the Physics repository (see msd.f90).

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Oct 30, 2017, at 4:29 AM, Nam Tran 
mailto:vnt...@uowmail.edu.au>> wrote:

Dear QE experts,

I am trying to evaluate MSD for my simulation.
My problem is that when an atom exits the simulation cell.
I do not know whether I should consider the distance with atom that goes about 
outside the box (a) or its image (b). Please check the image below (Blue is the 
original position t=0, red is the position at time t)


Best Regards
Nam Tran
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Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)

[Vahid Askarpour]

There is a collection of fortran codes (for VASP mainly but can easily be 
adapted) for processing simulation output including MSD calculation and the 
treatment of periodic images. They can be found at https://github.com/boates 
under the Physics repository (see msd.f90).

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Oct 30, 2017, at 4:29 AM, Nam Tran 
mailto:vnt...@uowmail.edu.au>> wrote:

Dear QE experts,

I am trying to evaluate MSD for my simulation.
My problem is that when an atom exits the simulation cell.
I do not know whether I should consider the distance with atom that goes about 
outside the box (a) or its image (b). Please check the image below (Blue is the 
original position t=0, red is the position at time t)


Best Regards
Nam Tran
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Re: [Pw_forum] phosphorene monolayer

[Vahid Askarpour]

I used the following reference: Scientific Reports, 5,8501,2015 by Jain and 
McGaughey.

Vahid


On Oct 5, 2017, at 6:24 PM, Gautam Gaddemane 
mailto:gautam...@gmail.com>> wrote:

Thank you so much Vahid. I have a question though..how did you get the initial 
CELL_PARAMETERS ? I obtained the initial cell and atomic parameters from bulk.

GAUTAM GADDEMANE
DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
UNIVERSITY OF TEXAS AT DALLAS

On Thu, Oct 5, 2017 at 4:19 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:
Hi Gautam,

The following relaxation input worked for me:

BP
2D
&control
calculation='vc-relax'
restart_mode='from_scratch',
prefix='BP'
pseudo_dir='./'
verbosity='high'
tprnfor=.true.
tstress=.true.
etot_conv_thr=1.0e-06
forc_conv_thr=1.0e-05
/
&system
ibrav=0,
nat= 4, ntyp= 1
ecutwfc = 50, ecutrho=200,
occupations = 'fixed' ,
/
&electrons
diagonalization='cg'
conv_thr = 1.0e-12
mixing_beta = 0.7
electron_maxstep = 500
mixing_mode = 'plain'
/
&IONS
  ion_dynamics = 'bfgs'
  pot_extrapolation='atomic'
  wfc_extrapolation='atomic'
/
&CELL
  cell_dynamics = 'bfgs'
  wmass=0.002
  cell_factor=2.0
  cell_dofree='xyz'
/
ATOMIC_SPECIES
P  30.97376  P.pbesol-n-kjpaw_psl.0.1.UPF

K_POINTS {automatic}
14 12 1  0 0 0

CELL_PARAMETERS (angstrom)
   4.429539231   0.0   0.0
   0.0   3.279402120   0.0
   0.0   0.0  31.941846246

ATOMIC_POSITIONS (crystal)
P0.001152971   0.0   0.015264978
P    0.335395312   0.49800   0.015264292
P0.501101273   0.49800   0.081335135
P0.835350444   0.0   0.081335495

Best,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

> On Oct 5, 2017, at 4:45 PM, Gautam Gaddemane 
> mailto:gautam...@gmail.com>> wrote:
>
> Dear All,
>
> I am trying to calculate the bands tructure for monolayer phosphorene and I 
> am just a week old in using quantum espresso.
> From the bulk unit cell I prepared an input file to relax the structure but I 
> was not able to get a good lattice constant nor a good band gap. It would be 
> very helpful if someone would guide me in this procedure.
> I have attahced the file I used to relax in this email
>
>
> &CONTROL
>   calculation='vc-relax',
>   outdir='./',
>   prefix='calc',
>   pseudo_dir='./',
>   verbosity='high',
> /
>
> &SYSTEM
>   ibrav=0,
>   celldm(1)= 8.276999830d0
>   nat=4,
>   ntyp=1,
>   ecutwfc=60,
>   ecutrho=360,
>   input_dft='lda',
>   occupations='smearing',
>   smearing='mv',
>   degauss=0.005d0,
> /
>
> &ELECTRONS
>   conv_thr=1d-06,
>   mixing_beta=0.7d0,
> /
> &IONS
>   ion_dynamics='bfgs'
> /
>
> &CELL
>   cell_dynamics='bfgs'
>   cell_dofree='2Dshape'
> /
> ATOMIC_SPECIES
>   P 30.973800d0 P.pw<http://P.pw>-mt_fhi.UPF
>
> ATOMIC_POSITIONS {crystal}
>
>  P  0.09004 0.0 0.050195117
>  P  0.90967 0.0 0.949804902
>  P  0.59033 0.5 0.949804902
>  P  0.40996 0.5 0.050195117
>
> K_POINTS {automatic}
>
>   12 12 1 0 0 0
>
> CELL_PARAMETERS {alat}
>
>  1.0.0.
>  0.0.7511415530000.
>  0.0.   4.680365292
>
>
> thank you
> Gautam
>
> GAUTAM GADDEMANE
> DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
> UNIVERSITY OF TEXAS AT DALLAS
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Re: [Pw_forum] phosphorene monolayer

[Vahid Askarpour]

Hi Gautam,

The following relaxation input worked for me:

BP
2D
&control
calculation='vc-relax'
restart_mode='from_scratch',
prefix='BP'
pseudo_dir='./'
verbosity='high'
tprnfor=.true.
tstress=.true.
etot_conv_thr=1.0e-06
forc_conv_thr=1.0e-05
/
&system
ibrav=0,
nat= 4, ntyp= 1
ecutwfc = 50, ecutrho=200,
occupations = 'fixed' , 
/
&electrons
diagonalization='cg'
conv_thr = 1.0e-12
mixing_beta = 0.7
electron_maxstep = 500
mixing_mode = 'plain'
/
&IONS
  ion_dynamics = 'bfgs'
  pot_extrapolation='atomic'
  wfc_extrapolation='atomic'
/
&CELL
  cell_dynamics = 'bfgs'
  wmass=0.002
  cell_factor=2.0
  cell_dofree='xyz'
/
ATOMIC_SPECIES
P  30.97376  P.pbesol-n-kjpaw_psl.0.1.UPF 

K_POINTS {automatic}
14 12 1  0 0 0

CELL_PARAMETERS (angstrom)
   4.429539231   0.0   0.0
   0.0   3.279402120   0.0
   0.0   0.0  31.941846246

ATOMIC_POSITIONS (crystal)
P0.001152971   0.0   0.015264978
P0.335395312   0.49800   0.015264292
P0.501101273   0.49800   0.081335135
P0.835350444   0.0   0.081335495

Best,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

> On Oct 5, 2017, at 4:45 PM, Gautam Gaddemane  wrote:
> 
> Dear All,
> 
> I am trying to calculate the bands tructure for monolayer phosphorene and I 
> am just a week old in using quantum espresso.
> From the bulk unit cell I prepared an input file to relax the structure but I 
> was not able to get a good lattice constant nor a good band gap. It would be 
> very helpful if someone would guide me in this procedure.
> I have attahced the file I used to relax in this email
> 
>  
> &CONTROL 
>   calculation='vc-relax', 
>   outdir='./', 
>   prefix='calc', 
>   pseudo_dir='./', 
>   verbosity='high', 
> / 
>  
> &SYSTEM 
>   ibrav=0,
>   celldm(1)= 8.276999830d0 
>   nat=4, 
>   ntyp=1, 
>   ecutwfc=60, 
>   ecutrho=360, 
>   input_dft='lda', 
>   occupations='smearing', 
>   smearing='mv', 
>   degauss=0.005d0, 
> / 
>  
> &ELECTRONS 
>   conv_thr=1d-06, 
>   mixing_beta=0.7d0, 
> / 
> &IONS 
>   ion_dynamics='bfgs' 
> / 
>  
> &CELL 
>   cell_dynamics='bfgs' 
>   cell_dofree='2Dshape'   
> / 
> ATOMIC_SPECIES 
>   P 30.973800d0 P.pw-mt_fhi.UPF 
>  
> ATOMIC_POSITIONS {crystal} 
>  
>  P  0.09004 0.0 0.050195117
>  P  0.90967 0.0 0.949804902
>  P  0.59033 0.5 0.949804902
>  P  0.40996 0.5 0.050195117 
>  
> K_POINTS {automatic} 
>  
>   12 12 1 0 0 0 
>  
> CELL_PARAMETERS {alat} 
>  
>  1.0.0. 
>  0.0.7511415530000. 
>  0.0.   4.680365292
> 
> 
> thank you
> Gautam
> 
> GAUTAM GADDEMANE
> DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
> UNIVERSITY OF TEXAS AT DALLAS
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[Pw_forum] Compiling qe-6.0 with -D__WANLIB

[Vahid Askarpour]

Dear QE Community,

In attempting to compile QE-6.0 with Wannier90 with the “library mode” 
capability, I added the -D__WANLIB to the DFLAGS in make.inc. When I issue 
“make pwall”, I get the following error:

pw2wannier90.o libpp.a ../../PW/src/libpw.a ../../Modules/libqemod.a 
../../FFTXlib/libqefft.a ../../LAXlib/libqela.a 
/home/vaskarpo/bin/qe-6.0_gcc//clib/clib.a 
/home/vaskarpo/bin/qe-6.0_gcc//iotk/src/libiotk.a -lmkl_scalapack_lp64 
-lmkl_blacs_openmpi_lp64   -lmkl_gf_lp64  -lmkl_sequential -lmkl_core
pw2wannier90.o: In function `run_wannier_':
/home/vaskarpo/bin/qe-6.0_gcc/PP/src/pw2wannier90.f90:636: undefined reference 
to `wannier_run_'
pw2wannier90.o: In function `setup_nnkp_':
/home/vaskarpo/bin/qe-6.0_gcc/PP/src/pw2wannier90.f90:511: undefined reference 
to `wannier_setup_'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:140: pw2wannier90.x] Error 1
make[2]: Leaving directory '/home/vaskarpo/bin/qe-6.0_gcc/PP/src'
make[1]: *** [Makefile:7: all] Error 1
make[1]: Leaving directory '/home/vaskarpo/bin/qe-6.0_gcc/PP'
make: *** [Makefile:92: pp] Error 1


I am using gcc/5.4.0 and openmpi/2.1.1 with mkl/11.3.4.258.

Is this not the correct way to build QE with Wannier90 in the library mode?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


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[Pw_forum] Compiling QE-6.0 on IOLENGTH=4 machine

[Vahid Askarpour]

Dear QE Users,

I have compiled QE-6.0 on a linux machine with intel-2016.4.258. The IOLENGTH 
on this machine is 4. So I changed the DIRECT_IO_FACTOR in the 
/Modules/io_files.f90 from 8 to 4. However, a simple self-consistent run 
crashed with the following error:

 from davcio : error #10
 error while writing from file 
"/scratch/vaskarpo/qe-6.0_LENGTH4/default_phonons/1/./SnSe.wfc19”

Are there other parts of the QE code that use IOLENGTH=8 (other than EPW and 
PP) explicitly without using DIRECT_IO_FACTOR as a parameter? In other words, 
are there other parts of the code that needs to change in order to get it to 
work on the above machine?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

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Re: [Pw_forum] Dielectric constant at RPA level with PHONON

[Vahid Askarpour]

Hi Stefano,

Thank you for taking the time to answer my question. Would you happen to have 
an input file that works with lrpa=.true. for the calculation of the 
macroscopic dielectric constant?

Best,

Vahid


On Jun 30, 2017, at 1:54 AM, stefano de gironcoli 
mailto:degir...@sissa.it>> wrote:

because somewhere in phq_readin
   trans = trans .OR. ldisp
lrpa is only valid for the calculation of the macroscopic dielectric
constant, not for the vibrational parts.

stefano

On 30/06/2017 01:06, Vahid Askarpour wrote:
Dear QE Users,

After a self consistent calculation, I used the following input to the ph.x 
code (qe-6.1) to calculate the dielectric constant at the RPA level using the 
lrpa tag.

SnSe
&inputph
  tr2_ph   =  1.0d-16
  prefix   = 'SnSe'
  amass(1) = 118.71
  amass(2) = 78.96
  ldisp = .true.
  epsil=.true.
  trans = .false.
  lrpa = .true.
  qplot = .true.
  outdir   = './'
  alpha_mix(1)=0.3
  fildyn   = 'SnSe.dyn'
  fildvscf = 'dvscf'
 /
 48
   0.000   0.000   0.000   0.0138889
   0.000   0.000   0.167   0.028
   0.000   0.000   0.333   0.028
   0.000   0.000  -0.500   0.0138889
   0.000   0.167   0.000   0.028
   0.000   0.167   0.167   0.056
   0.000   0.167   0.333   0.056
   0.000   0.167  -0.500   0.028
   0.000   0.333   0.000   0.028
   0.000   0.333   0.167   0.056
   0.000   0.333   0.333   0.056
   0.000   0.333  -0.500   0.028
   0.000  -0.500   0.000   0.0138889
   0.000  -0.500   0.167   0.028
   0.000  -0.500   0.333   0.028
   0.000  -0.500  -0.500   0.0138889
   0.250   0.000   0.000   0.028
   0.250   0.000   0.167   0.056
   0.250   0.000   0.333   0.056
   0.250   0.000  -0.500   0.028
   0.250   0.167   0.000   0.056
   0.250   0.167   0.167   0.111
   0.250   0.167   0.333   0.111
   0.250   0.167  -0.500   0.056
   0.250   0.333   0.000   0.056
   0.250   0.333   0.167   0.111
   0.250   0.333   0.333   0.111
   0.250   0.333  -0.500   0.056
   0.250  -0.500   0.000   0.028
   0.250  -0.500   0.167   0.056
   0.250  -0.500   0.333   0.056
   0.250  -0.500  -0.500   0.028
  -0.500   0.000   0.000   0.0138889
  -0.500   0.000   0.167   0.028
  -0.500   0.000   0.333   0.028
  -0.500   0.000  -0.500   0.0138889
  -0.500   0.167   0.000   0.028
  -0.500   0.167   0.167   0.056
  -0.500   0.167   0.333   0.056
  -0.500   0.167  -0.500   0.028
  -0.500   0.333   0.000   0.028
  -0.500   0.333   0.167   0.056
  -0.500   0.333   0.333   0.056
  -0.500   0.333  -0.500   0.028
  -0.500  -0.500   0.000   0.0138889
  -0.500  -0.500   0.167   0.028
  -0.500  -0.500   0.333   0.028
  -0.500  -0.500  -0.500   0.0138889

I get the following error:

 %

 task # 6  from phq_readin : error # 1
 only dielectric constant with lrpa or lnoloc
 %

I checked the phq_redin.f90 code and the error arises from the following line:

  IF (trans.AND.(lrpa.OR.lnoloc)) CALL errore('phq_readin', &
'only dielectric constant with lrpa or lnoloc',1)

Since I have set trans=.false., why am I getting this error? There must be 
something wrong with the input but no such error was reported to the Forum.

Any suggestions would be appreciated.

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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[Pw_forum] Dielectric constant at RPA level with PHONON

[Vahid Askarpour]

Dear QE Users,

After a self consistent calculation, I used the following input to the ph.x 
code (qe-6.1) to calculate the dielectric constant at the RPA level using the 
lrpa tag.

SnSe
&inputph
  tr2_ph   =  1.0d-16
  prefix   = 'SnSe'
  amass(1) = 118.71
  amass(2) = 78.96 
  ldisp = .true.
  epsil=.true.
  trans = .false.
  lrpa = .true.
  qplot = .true.
  outdir   = './'
  alpha_mix(1)=0.3
  fildyn   = 'SnSe.dyn'
  fildvscf = 'dvscf'
 /
 48
   0.000   0.000   0.000   0.0138889
   0.000   0.000   0.167   0.028
   0.000   0.000   0.333   0.028
   0.000   0.000  -0.500   0.0138889
   0.000   0.167   0.000   0.028
   0.000   0.167   0.167   0.056
   0.000   0.167   0.333   0.056
   0.000   0.167  -0.500   0.028
   0.000   0.333   0.000   0.028
   0.000   0.333   0.167   0.056
   0.000   0.333   0.333   0.056
   0.000   0.333  -0.500   0.028
   0.000  -0.500   0.000   0.0138889
   0.000  -0.500   0.167   0.028
   0.000  -0.500   0.333   0.028
   0.000  -0.500  -0.500   0.0138889
   0.250   0.000   0.000   0.028
   0.250   0.000   0.167   0.056
   0.250   0.000   0.333   0.056
   0.250   0.000  -0.500   0.028
   0.250   0.167   0.000   0.056
   0.250   0.167   0.167   0.111
   0.250   0.167   0.333   0.111
   0.250   0.167  -0.500   0.056
   0.250   0.333   0.000   0.056
   0.250   0.333   0.167   0.111
   0.250   0.333   0.333   0.111
   0.250   0.333  -0.500   0.056
   0.250  -0.500   0.000   0.028
   0.250  -0.500   0.167   0.056
   0.250  -0.500   0.333   0.056
   0.250  -0.500  -0.500   0.028
  -0.500   0.000   0.000   0.0138889
  -0.500   0.000   0.167   0.028
  -0.500   0.000   0.333   0.028
  -0.500   0.000  -0.500   0.0138889
  -0.500   0.167   0.000   0.028
  -0.500   0.167   0.167   0.056
  -0.500   0.167   0.333   0.056
  -0.500   0.167  -0.500   0.028
  -0.500   0.333   0.000   0.028
  -0.500   0.333   0.167   0.056
  -0.500   0.333   0.333   0.056
  -0.500   0.333  -0.500   0.028
  -0.500  -0.500   0.000   0.0138889
  -0.500  -0.500   0.167   0.028
  -0.500  -0.500   0.333   0.028
  -0.500  -0.500  -0.500   0.0138889

I get the following error:

 %

 task # 6  from phq_readin : error # 1
 only dielectric constant with lrpa or lnoloc
 %

I checked the phq_redin.f90 code and the error arises from the following line:

  IF (trans.AND.(lrpa.OR.lnoloc)) CALL errore('phq_readin', &
'only dielectric constant with lrpa or lnoloc',1)

Since I have set trans=.false., why am I getting this error? There must be 
something wrong with the input but no such error was reported to the Forum.

Any suggestions would be appreciated.

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] Potential plot for SnSe

[Vahid Askarpour]

Let me share what I have found so far. I hope someone can at least verify if 
the following is correct:

1. in plot_1d routine of chdens.f90, the plotted x-axis is deltax*dble(i-1).
2. deltax = m1 / (nx - 1)
3. and m1 = sqrt (e1 (1)**2 + e1 (2)**2 + e1 (3)**2)

So in my case, m1, which is the modulus of e1=0.333 in alat units. That’s why 
the x-axis runs from 0 to ~0.33. However, the origin of the plot is (0,0,0) and 
not x0.

Thank you,

Vahid


On Jun 20, 2017, at 4:12 PM, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Just a correction to my pp.x input file:

I actually used cartesian coordinates for the e1 and x0. So

0.3571863   0.2721583   0.1838386 for x0 and
0.1171583   0.2721583   0.1535005  for e1.

Vahid




Feedback<http://aka.ms/SafetyTipsFeedback>
Dear QE Users,

In order to calculate the total potential along one of the SnSe bonds 
(Se2-Sn4), I first performed a self-consistent run with the following lattice 
parameters.

ibrav=8, celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894

Sn   0.882841736   0.25000   0.602195343
Sn   0.617158264   0.75000   0.102195343
Sn   0.382841736   0.25000   0.897804657
Sn   0.117158264   0.75000   0.397804657
Se   0.142813748   0.25000   0.976427467
Se   0.357186252   0.75000   0.476427467
Se   0.642813748   0.25000   0.523572533
Se   0.857186252   0.75000   0.023572533

I then ran pp.x with the following input:

&inputpp
prefix  = 'SnSe'
filplot = 'potential.dat'
plot_num= 1
/
&plot
  iflag=1
  output_format=0
  nfile = 1
  filepp(1) = 'potential.dat'
  e1(1)=0.117158264,  e1(2)=0.75000,  e1(3)= 0.397804657,
  x0(1)=0.357186252,  x0(2)= 0.75000,  x0(3)=0.476427467,
  nx=100,
  fileout= 'VSe2_Sn4.dat’
/

The bond length is 2.73A=5.16Bohr. Attached is the output of potential vs. 
distance. The x-axis runs from 0 to ~0.33. According to other links in the 
Forum, the x-axis is in atomic units. Two possibilities:

1. The distance is in Bohr. So is the pp.x code plotting from 0 to 0.33 Bohr 
even though the bond length is 5.16Bohr as defined by the vectors x0 and e1?
2. The distance is in alat. Then 0.33*alat=7.04Bohr. This is longer than the 
bond length.

So what is the unit of the x-axis?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada




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Re: [Pw_forum] Potential plot for SnSe

[Vahid Askarpour]

Just a correction to my pp.x input file:

I actually used cartesian coordinates for the e1 and x0. So

0.3571863   0.2721583   0.1838386 for x0 and
0.1171583   0.2721583   0.1535005  for e1.

Vahid




Feedback<http://aka.ms/SafetyTipsFeedback>
Dear QE Users,

In order to calculate the total potential along one of the SnSe bonds 
(Se2-Sn4), I first performed a self-consistent run with the following lattice 
parameters.

ibrav=8, celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894

Sn   0.882841736   0.25000   0.602195343
Sn   0.617158264   0.75000   0.102195343
Sn   0.382841736   0.25000   0.897804657
Sn   0.117158264   0.75000   0.397804657
Se   0.142813748   0.25000   0.976427467
Se   0.357186252   0.75000   0.476427467
Se   0.642813748   0.25000   0.523572533
Se   0.857186252   0.75000   0.023572533

I then ran pp.x with the following input:

&inputpp
prefix  = 'SnSe'
filplot = 'potential.dat'
plot_num= 1
/
&plot
  iflag=1
  output_format=0
  nfile = 1
  filepp(1) = 'potential.dat'
  e1(1)=0.117158264,  e1(2)=0.75000,  e1(3)= 0.397804657,
  x0(1)=0.357186252,  x0(2)= 0.75000,  x0(3)=0.476427467,
  nx=100,
  fileout= 'VSe2_Sn4.dat’
/

The bond length is 2.73A=5.16Bohr. Attached is the output of potential vs. 
distance. The x-axis runs from 0 to ~0.33. According to other links in the 
Forum, the x-axis is in atomic units. Two possibilities:

1. The distance is in Bohr. So is the pp.x code plotting from 0 to 0.33 Bohr 
even though the bond length is 5.16Bohr as defined by the vectors x0 and e1?
2. The distance is in alat. Then 0.33*alat=7.04Bohr. This is longer than the 
bond length.

So what is the unit of the x-axis?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada




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[Pw_forum] Potential plot for SnSe

[Vahid Askarpour]

Dear QE Users,

In order to calculate the total potential along one of the SnSe bonds 
(Se2-Sn4), I first performed a self-consistent run with the following lattice 
parameters.

ibrav=8, celldm(1)=21.34350847, celldm(2)=0.3628777, celldm(3)=0.38586894

Sn   0.882841736   0.25000   0.602195343
Sn   0.617158264   0.75000   0.102195343
Sn   0.382841736   0.25000   0.897804657
Sn   0.117158264   0.75000   0.397804657
Se   0.142813748   0.25000   0.976427467
Se   0.357186252   0.75000   0.476427467
Se   0.642813748   0.25000   0.523572533
Se   0.857186252   0.75000   0.023572533

I then ran pp.x with the following input:

&inputpp
prefix  = 'SnSe'
filplot = 'potential.dat'
plot_num= 1
/
&plot
  iflag=1
  output_format=0
  nfile = 1
  filepp(1) = 'potential.dat'
  e1(1)=0.117158264,  e1(2)=0.75000,  e1(3)= 0.397804657,
  x0(1)=0.357186252,  x0(2)= 0.75000,  x0(3)=0.476427467,
  nx=100,
  fileout= 'VSe2_Sn4.dat’
/

The bond length is 2.73A=5.16Bohr. Attached is the output of potential vs. 
distance. The x-axis runs from 0 to ~0.33. According to other links in the 
Forum, the x-axis is in atomic units. Two possibilities:

1. The distance is in Bohr. So is the pp.x code plotting from 0 to 0.33 Bohr 
even though the bond length is 5.16Bohr as defined by the vectors x0 and e1?
2. The distance is in alat. Then 0.33*alat=7.04Bohr. This is longer than the 
bond length.

So what is the unit of the x-axis?

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada






SnSe_potential.pdf
Description: SnSe_potential.pdf
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Re: [Pw_forum] Overlap integral for periodic part of eigenfunction

[Vahid Askarpour]

Dear Lorenzo,

Thank you so much for pointing out the pw2wannier90.x code. I have seen this 
code in the wannier90-2.0.1/pwscf/v5.0
folder and it only calculates the overlap for the nearest neighbor k-points 
(loops over nnb in the compute_mmn subroutine). The one you referred to does 
not have this limitation. I will give it a try.

Best wishes,

Vahid


> On Mar 16, 2017, at 5:14 AM, Lorenzo Paulatto 
>  wrote:
> 
> On Wednesday, March 15, 2017 11:11:54 PM CET Vahid Askarpour wrote:
>> I would like to calculate the overlap integral  u*_k’(r)u_k(r)d^3r. 
> 
> Dear Vahid,
> if you want to do it for excercize, go on and do it.
> 
> But, you may be happy to know that this integral is already computed in 
> several places in the pw code. One in particular is the pw2wannier90.x code 
> in 
> particular in  PP/src/pw2wannier90.f90 from line 2120 to line 2187
> 
> (and in general all the compute_mmn subroutine, but it does also a few more 
> operations and some parts related to ultrasoft pseudopotentials are a bit 
> difficult to understand)
> 
>> 1. Am I correct in assuming that the above integral is equivalent to the
>> sum(C*_k C_k’), where C’s are the coefficients from evc.dat and the sum is 
>> over igwx (maximum G-vector index) specified in eve.dat? 
> 
> No, i I remember correctly the wfcs on files are in G-space. Doing the 
> product 
> in G-space is equivalent to doing a convolution in real space.
> 
>> 2. igwx is different for different k-points. One k-point may have igwx=1459
>> while another k-point has igwx=1468. In the above sum, is it correct to 
>> to use the top 1468 coefficients of the first k-point to calculate the 
>> overlap
>> integral between the two k-points?
> 
> No, because the order is not necessarily the same. Also, because you wouldn't 
> be doing the product of the two functions but their convolution.
> 
> hth
> 
> 
> -- 
> 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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[Pw_forum] Overlap integral for periodic part of eigenfunction

[Vahid Askarpour]

Dear QE Community,

We know that |psi(k,r)> =u(r)exp(ik.r), where u(r) has the periodicity of the 
lattice. The index k includes band index as well.

I would like to calculate the overlap integral  u*_k’(r)u_k(r)d^3r. To this 
end, I have extracted the real and imaginary parts of
wave function coefficients from evc.dat for all the k-points and bands by 
setting wf_collect=.true..

I have two questions:

1. Am I correct in assuming that the above integral is equivalent to the 
sum(C*_k C_k’), where C’s are the coefficients from evc.dat and the sum is
over igwx (maximum G-vector index) specified in eve.dat?

2. igwx is different for different k-points. One k-point may have igwx=1459 
while another k-point has igwx=1468. In the above sum, is it correct to
to use the top 1468 coefficients of the first k-point to calculate the overlap 
integral between the two k-points?


An earlier post (http://qe-forge.org/pipermail/pw_forum/2015-April/106663.html) 
suggests a similar concept for   but not for .

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada

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[Pw_forum] Irreducible Representation for a list of q-points

[Vahid Askarpour]

Dear QE Users,

When using the ph.x code, the output shows the label for the irreducible 
representation for each mode, such as T_1g or T_1u as done in the 
divide_class.f90 routine of the PW/src. When putting a list of say 2000 
q-points into matdyn.x, I can get the eigenvectors for each mode.

Is there a tag or a post-processing tool which allows the determination of the 
irreducible representation label for the modes associated with each of those 
2000 q-points? If not, is it possible to extract the table for irreducible 
representation for all the modes of a list of q-points in QE?



Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] alpha_mix alters phonon frequencies in GaAs

[Vahid Askarpour]

Dear Professor Marzari,

I tried tr2_ph=10^-16 for the three q-points I reported earlier and now the two 
sets give almost identical results. I do get -1.661923 cm^-1 for 
alpha_mix(1)=0.7 and -1.465509 cm^-1 for alpha_mix(1)=0.3 for the three 
acoustic modes at the zone center but I guess that is reasonable and requires 
ASR treatment. All the other modes are consistent between the two sets.

Thank you for your help.

Vahid

On Jan 13, 2017, at 10:37 AM, Marzari Nicola 
mailto:nicola.marz...@epfl.ch>> wrote:

Try tr2A_ph 10^-14, or -16, and report!

Thanks

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

On 13 Jan 2017, at 15:35, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear QE Community,

I have compiled qe-6.0 with intel-14 and openmpi-1.6.5. In attempting to speed 
up the phonon calculation (as suggested in other posts), I have tried two 
different alpha_mix(1) values- the default value of 0.7 and 0.3. For Si, the 
two alpha_mix values give almost identical phonon frequencies for all q-points. 
For GaAs, I get different frequencies. I suspect it may be due to the LO-TO 
splitting at the zone center but the differences exist for other q-points as 
well particularly for the acoustic modes.

For example, for q=(0,0,0), I get the following frequencies in wavenumber in 
the .dyn files:
alpha_mix(1)=0.7 : 5.936331, 5.936331, 5.936331, 
249.858731,249.858731,249.858731
alpha_mix(1)=0.3 : -17.197390, -17.197390,-17.197390, 247.538697, 247.538697, 
247.538697

For q=(0.125,-0.125,0.125) I get:
alpha_mix(1)=0.7 : 31.681603, 31.681603, 62.388768, 246.723626, 246.723626, 
266.652186
alpha_mix(1)=0.3 : 34.440636, 34.440636, 62.925154, 247.034644, 247.034644, 
266.813369


For q=(-0.25,0.25,-0.25) I get:
alpha_mix(1)=0.7 : 49.997159, 49.997159, 120.235286, 242.448112, 242.448112, 
255.746902
alpha_mix(1)=0.3 : 52.457875, 52.457875, 121.042662, 242.645430, 242.645430, 
255.836026

The issue of negative phonon frequencies has been exhaustively discussed on the 
forum and is not the point of my post. I assume that  alpha_mix is not a 
convergence parameter and  should not change the frequencies but it does. I 
have also run on SnSe where I do not get negative frequencies at all for either 
alpha_mix values but the frequencies differ by 10-20 wavenumbers between the 
two sets. I should add that all self-consistent calculations for the individual 
modes reached convergence. Convergence tests were done for the cutoff energy 
and K-grid as well.

Here are my input files for the initial self-consistent run followed by the 
phonon calculation:


 &control
calculation = 'scf'
prefix  = 'gaas'
restart_mode= 'from_scratch'
wf_collect  = .false.
pseudo_dir  = './'
outdir  = './'
verbosity   = 'high'
tprnfor = .true.
tstress = .true.
 /
 &system
ibrav=2,celldm(1)=10.838928,
nat= 2, ntyp= 2 , nbnd=16
ecutwfc = 70, ecutrho=280,
occupations = 'fixed'
 /
 &electrons
diagonalization = 'david'
mixing_beta = 0.7
conv_thr= 1.0d-10
 /
ATOMIC_SPECIES
Ga   69.723   Ga.pbe-hgh.UPF
As   74.92160 As.pbe-hgh.UPF
ATOMIC_POSITIONS  crystal
  Ga 0.0   0.0   0.0
  As -0.25  0.75  -0.25
K_POINTS   automatic
   12 12 12 0 0 0

==

GaAs
&inputph
  tr2_ph   =  1.0d-12
  prefix   = 'gaas'
  amass(1) = 69.723
  amass(2) = 74.92160
  ldisp = .true.
  epsil = .true.
  nq1=8, nq2=8, nq3=8
  outdir   = './'
  alpha_mix(1)=0.3
  fildyn   = 'gaas.dyn'
  fildvscf = 'dvscf'
 /
===

I would appreciate any input as to why alpha_mix alters the results for polar 
materials such as GaAs and SnSe.

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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[Pw_forum] alpha_mix alters phonon frequencies in GaAs

[Vahid Askarpour]

Dear QE Community,

I have compiled qe-6.0 with intel-14 and openmpi-1.6.5. In attempting to speed 
up the phonon calculation (as suggested in other posts), I have tried two 
different alpha_mix(1) values- the default value of 0.7 and 0.3. For Si, the 
two alpha_mix values give almost identical phonon frequencies for all q-points. 
For GaAs, I get different frequencies. I suspect it may be due to the LO-TO 
splitting at the zone center but the differences exist for other q-points as 
well particularly for the acoustic modes.

For example, for q=(0,0,0), I get the following frequencies in wavenumber in 
the .dyn files:
alpha_mix(1)=0.7 : 5.936331, 5.936331, 5.936331, 
249.858731,249.858731,249.858731
alpha_mix(1)=0.3 : -17.197390, -17.197390,-17.197390, 247.538697, 247.538697, 
247.538697

For q=(0.125,-0.125,0.125) I get:
alpha_mix(1)=0.7 : 31.681603, 31.681603, 62.388768, 246.723626, 246.723626, 
266.652186
alpha_mix(1)=0.3 : 34.440636, 34.440636, 62.925154, 247.034644, 247.034644, 
266.813369


For q=(-0.25,0.25,-0.25) I get:
alpha_mix(1)=0.7 : 49.997159, 49.997159, 120.235286, 242.448112, 242.448112, 
255.746902
alpha_mix(1)=0.3 : 52.457875, 52.457875, 121.042662, 242.645430, 242.645430, 
255.836026

The issue of negative phonon frequencies has been exhaustively discussed on the 
forum and is not the point of my post. I assume that  alpha_mix is not a 
convergence parameter and  should not change the frequencies but it does. I 
have also run on SnSe where I do not get negative frequencies at all for either 
alpha_mix values but the frequencies differ by 10-20 wavenumbers between the 
two sets. I should add that all self-consistent calculations for the individual 
modes reached convergence. Convergence tests were done for the cutoff energy 
and K-grid as well.

Here are my input files for the initial self-consistent run followed by the 
phonon calculation:


 &control
calculation = 'scf'
prefix  = 'gaas'
restart_mode= 'from_scratch'
wf_collect  = .false.
pseudo_dir  = './'
outdir  = './'
verbosity   = 'high'
tprnfor = .true.
tstress = .true.
 /
 &system
ibrav=2,celldm(1)=10.838928,
nat= 2, ntyp= 2 , nbnd=16
ecutwfc = 70, ecutrho=280,
occupations = 'fixed'
 /
 &electrons
diagonalization = 'david'
mixing_beta = 0.7
conv_thr= 1.0d-10
 /
ATOMIC_SPECIES
Ga   69.723   Ga.pbe-hgh.UPF
As   74.92160 As.pbe-hgh.UPF
ATOMIC_POSITIONS  crystal
  Ga 0.0   0.0   0.0
  As -0.25  0.75  -0.25
K_POINTS   automatic
   12 12 12 0 0 0

==

GaAs
&inputph
  tr2_ph   =  1.0d-12
  prefix   = 'gaas'
  amass(1) = 69.723
  amass(2) = 74.92160
  ldisp = .true.
  epsil = .true.
  nq1=8, nq2=8, nq3=8
  outdir   = './'
  alpha_mix(1)=0.3
  fildyn   = 'gaas.dyn'
  fildvscf = 'dvscf'
 /
===

I would appreciate any input as to why alpha_mix alters the results for polar 
materials such as GaAs and SnSe.

Thank you,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Hi Ye,

I reinstalled the QE/EPW package from scratch and now the segfault does not 
occur. Before, I only compiled EPW by issuing make in the EPW folder. This 
time, I issued “make epw” from the QE
folder to rebuild both. Odd!

I did print kunit and nbase. Kunit is 1 and nbase is one of the following (not 
in the order below though) when run on 8 cpus:

0, 6, 12, 18, 24, 30, 36, 42, and 47.

Thank you for all the suggestions you made and best wishes,

Vahid


On Oct 30, 2016, at 10:03 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

Is kunit=1 ?
Is your nkf and nkf_tot the same as nks nks_tot provided by QE environment?
Could you print the nbase for each processor and see if they are the numbers 
expected?

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-30 18:59 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
I allocate an array that needs to be calculated among pools using:

ALLOCATE(A(3,nbnd,nkf)), where nkf is the number of k points per pool and 
initialized as:
A(:,:,:)=0

Once array A is calculated, I allocate array A_tot as:

ALLOCATE(A_tot(3,nbnd,nkf_tot)), where nkf_tot is the total number of k points. 
and initialized as:
A_tot(:,:,:)=0

Then I call the poolgather1 as below:

#if defined(__MPI)
CALL poolgather1(3,nbnd,nkf_tot,nkf,A,A_tot)
#else
A_tot=A
#endif

I have tried both allocating A_tot outside and inside the #if defined section.

Poolgather1 is similar to other EPW poolgather and QE poolcollect routines and 
is given below:

subroutine poolgather1 (nsize1,nsize2,nkstot,nks, f_in, f_out)
  !
  USE kinds, ONLY : DP
  USE mp_global, ONLY : my_pool_id, inter_pool_comm, npool,kunit
  USE mp,ONLY : mp_barrier, mp_bcast,mp_sum
  USE mp_world,  ONLY : mpime
  implicit none
  !
  INTEGER, INTENT (in) :: nsize1
  !! first dimension of vectors f_in and f_out
  INTEGER, INTENT (in) :: nsize2
  !! second dimension of vectors f_in and f_out
  INTEGER, INTENT (in) :: nks
  !! number of k-points per pool
  INTEGER, INTENT (in) :: nkstot
  !! total number of k-points
  REAL (KIND=DP), INTENT (in) :: f_in(nsize1,nsize2,nks)
  ! input ( only for k-points of mypool )
  REAL (KIND=DP), INTENT (out)  :: f_out(nsize1,nsize2,nkstot)
  ! output  ( contains values for all k-point )
  !
#if defined(__MPI)
  INTEGER :: rest, nbase
  ! the rest of the integer division nkstot / npool
  ! the position in the original list
  rest = nkstot / kunit - ( nkstot / kunit / npool ) * npool
  !
  nbase = nks * my_pool_id
  !
  IF ( ( my_pool_id + 1 ) > rest ) nbase = nbase + rest * kunit
  !
  f_out = 0.d0
  f_out(1:nsize1,1:nsize2,(nbase+1):(nbase+nks)) = f_in(1:nsize1,1:nsize2,1:nks)
  !
  ! ... reduce across the pools
  !
  CALL mp_sum(f_out,inter_pool_comm)
  !
#else
  f_out(:,:,:) = f_in(:,:,:)
  !
#endif
  !
  end subroutine poolgather1

For my test case, nsize1=3, nsize2=4, nkstot=47.

Thanks,

Vahid




On Oct 30, 2016, at 8:19 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

mp_sum_rt is interfaced with mp_sum for 3d array. When you mp_sum a 3d array, 
it will be automatically called.
USE mp,   ONLY : mp_sum_rt is not necessary.
If you want to check if mp_sum_rt is implicitly called via interface, you can 
print something before and after your mp_sum call and also print something in 
mp_sum_rt. You should find the expected printing behaviour.

if you compare the mp_sum_rt with the 2d and 4d implementation mp_sum_rm and 
mp_sum_r4d, you should find they flat the dimensionality and call the same 1-d 
routine reduce_base_real.

As I asked earlier, how did you allocate your 3-D arrays input and output? Are 
you allocating sufficient size for the output, did you deallocate it by 
mistake? How large is output array size, if it exceeds 2^32, you might hit the 
32bit integer bug of the variable msglen.

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-30 14:25 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Hi Ye,

The changes I am making are part of the EPW/QE code and so the parallelization 
depends on the QE MPI routines. I have no problem using mp_sum for a 2-D array 
such as
energy(iband,ik). I can use mp_sum to add the contributions from various nodes 
and print the total in agreement with the output from the serial run. As far as 
the allocation goes, I use the same 2-D approach to my 3-D array.

The problem arises when I use the 3-D array with mp_sum. I noticed that in the 
Modules/mp.f90 file, there is a subroutine as follows:

  SUBROUTINE mp_sum_rt( msg, gid )
IMPLICIT NONE
REAL (DP), INTENT (INOUT) :: msg(:,:,:)
INTEGER, INTENT(IN) :: gid
#if defined(__MPI)
INTEGER :: msglen
msglen = size(msg)
CALL reduce_base_real( msglen, msg, gid, -1 )
#endif
  END SUBROUTINE mp_sum_rt


Here  msg has three dimensions. There are other 

Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

I allocate an array that needs to be calculated among pools using:

ALLOCATE(A(3,nbnd,nkf)), where nkf is the number of k points per pool and 
initialized as:
A(:,:,:)=0

Once array A is calculated, I allocate array A_tot as:

ALLOCATE(A_tot(3,nbnd,nkf_tot)), where nkf_tot is the total number of k points. 
and initialized as:
A_tot(:,:,:)=0

Then I call the poolgather1 as below:

#if defined(__MPI)
CALL poolgather1(3,nbnd,nkf_tot,nkf,A,A_tot)
#else
A_tot=A
#endif

I have tried both allocating A_tot outside and inside the #if defined section.

Poolgather1 is similar to other EPW poolgather and QE poolcollect routines and 
is given below:

subroutine poolgather1 (nsize1,nsize2,nkstot,nks, f_in, f_out)
  !
  USE kinds, ONLY : DP
  USE mp_global, ONLY : my_pool_id, inter_pool_comm, npool,kunit
  USE mp,ONLY : mp_barrier, mp_bcast,mp_sum
  USE mp_world,  ONLY : mpime
  implicit none
  !
  INTEGER, INTENT (in) :: nsize1
  !! first dimension of vectors f_in and f_out
  INTEGER, INTENT (in) :: nsize2
  !! second dimension of vectors f_in and f_out
  INTEGER, INTENT (in) :: nks
  !! number of k-points per pool
  INTEGER, INTENT (in) :: nkstot
  !! total number of k-points
  REAL (KIND=DP), INTENT (in) :: f_in(nsize1,nsize2,nks)
  ! input ( only for k-points of mypool )
  REAL (KIND=DP), INTENT (out)  :: f_out(nsize1,nsize2,nkstot)
  ! output  ( contains values for all k-point )
  !
#if defined(__MPI)
  INTEGER :: rest, nbase
  ! the rest of the integer division nkstot / npool
  ! the position in the original list
  rest = nkstot / kunit - ( nkstot / kunit / npool ) * npool
  !
  nbase = nks * my_pool_id
  !
  IF ( ( my_pool_id + 1 ) > rest ) nbase = nbase + rest * kunit
  !
  f_out = 0.d0
  f_out(1:nsize1,1:nsize2,(nbase+1):(nbase+nks)) = f_in(1:nsize1,1:nsize2,1:nks)
  !
  ! ... reduce across the pools
  !
  CALL mp_sum(f_out,inter_pool_comm)
  !
#else
  f_out(:,:,:) = f_in(:,:,:)
  !
#endif
  !
  end subroutine poolgather1

For my test case, nsize1=3, nsize2=4, nkstot=47.

Thanks,

Vahid




On Oct 30, 2016, at 8:19 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

mp_sum_rt is interfaced with mp_sum for 3d array. When you mp_sum a 3d array, 
it will be automatically called.
USE mp,   ONLY : mp_sum_rt is not necessary.
If you want to check if mp_sum_rt is implicitly called via interface, you can 
print something before and after your mp_sum call and also print something in 
mp_sum_rt. You should find the expected printing behaviour.

if you compare the mp_sum_rt with the 2d and 4d implementation mp_sum_rm and 
mp_sum_r4d, you should find they flat the dimensionality and call the same 1-d 
routine reduce_base_real.

As I asked earlier, how did you allocate your 3-D arrays input and output? Are 
you allocating sufficient size for the output, did you deallocate it by 
mistake? How large is output array size, if it exceeds 2^32, you might hit the 
32bit integer bug of the variable msglen.

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-30 14:25 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Hi Ye,

The changes I am making are part of the EPW/QE code and so the parallelization 
depends on the QE MPI routines. I have no problem using mp_sum for a 2-D array 
such as
energy(iband,ik). I can use mp_sum to add the contributions from various nodes 
and print the total in agreement with the output from the serial run. As far as 
the allocation goes, I use the same 2-D approach to my 3-D array.

The problem arises when I use the 3-D array with mp_sum. I noticed that in the 
Modules/mp.f90 file, there is a subroutine as follows:

  SUBROUTINE mp_sum_rt( msg, gid )
IMPLICIT NONE
REAL (DP), INTENT (INOUT) :: msg(:,:,:)
INTEGER, INTENT(IN) :: gid
#if defined(__MPI)
INTEGER :: msglen
msglen = size(msg)
CALL reduce_base_real( msglen, msg, gid, -1 )
#endif
  END SUBROUTINE mp_sum_rt


Here  msg has three dimensions. There are other subroutines for 1, 2, and 4 
dimensions. Somehow, if I can get  EPW to use the above subroutine, it might 
work. Adding a statement like:

USE mp,   ONLY : mp_sum_rt

at the beginning of the file does not work as the compilation fails because EPW 
does not see the subroutine. Interestingly, it does see mp_sum which is in the 
same mp.f90 file.

So is there a way that I can get EPW to see mp_sum_rt? This might solve my 
problem.

Since I know that mp_sum works with 2-D arrays, one option is to rewrite my 
files in 2-D, one array for each x,y,z direction. I am trying to avoid this.

Thanks,

Vahid


On Oct 30, 2016, at 3:59 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

Hi Vahid,
segfault in mp_sum doesn't necessarily mean a problem there. Probably you wrote 
something to output array but not in a valid place before mp_sum.
Try to check your allocation of output and the copy make 

Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Hi Ye,

The changes I am making are part of the EPW/QE code and so the parallelization 
depends on the QE MPI routines. I have no problem using mp_sum for a 2-D array 
such as
energy(iband,ik). I can use mp_sum to add the contributions from various nodes 
and print the total in agreement with the output from the serial run. As far as 
the allocation goes, I use the same 2-D approach to my 3-D array.

The problem arises when I use the 3-D array with mp_sum. I noticed that in the 
Modules/mp.f90 file, there is a subroutine as follows:

  SUBROUTINE mp_sum_rt( msg, gid )
IMPLICIT NONE
REAL (DP), INTENT (INOUT) :: msg(:,:,:)
INTEGER, INTENT(IN) :: gid
#if defined(__MPI)
INTEGER :: msglen
msglen = size(msg)
CALL reduce_base_real( msglen, msg, gid, -1 )
#endif
  END SUBROUTINE mp_sum_rt


Here  msg has three dimensions. There are other subroutines for 1, 2, and 4 
dimensions. Somehow, if I can get  EPW to use the above subroutine, it might 
work. Adding a statement like:

USE mp,   ONLY : mp_sum_rt

at the beginning of the file does not work as the compilation fails because EPW 
does not see the subroutine. Interestingly, it does see mp_sum which is in the 
same mp.f90 file.

So is there a way that I can get EPW to see mp_sum_rt? This might solve my 
problem.

Since I know that mp_sum works with 2-D arrays, one option is to rewrite my 
files in 2-D, one array for each x,y,z direction. I am trying to avoid this.

Thanks,

Vahid


On Oct 30, 2016, at 3:59 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

Hi Vahid,
segfault in mp_sum doesn't necessarily mean a problem there. Probably you wrote 
something to output array but not in a valid place before mp_sum.
Try to check your allocation of output and the copy make sure they are correct.

Ye


===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-28 14:33 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Hi Ye,

Thank you for your suggestion. I tried it and when I ran the code, it 
seg-faulted. I put flags in the code to see where the segmentation faults 
occurs. It happens as the code calls mp_sum. It seems that mp_sum may not
be able to handle this reduction.

Cheers,
Vahid

On Oct 28, 2016, at 2:51 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

In Fortran, whatever-D array is 1-D array. mp_sum should be fine.
I saw something strange in your code that you were not copying the right things 
as you expected.
How about the following?
output(1:3,1:nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(1:3,1:nbnds,1:k_pool)

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-28 12:29 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Dear QE Users,

I am working on some modifications to the QE-6.0 code using symmetry. When I 
try to combine a 3-D array scattered across nodes, I use the following:

output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(3,nbnds,1:k_pool)

Here, nbnds is the number of bands, k_pool is the number of k points/pool, and 
pool_id is the id of the pool. Here I am assuming the the number of k points is 
divisible by the number of pools.

Then I call mp_sum(output,inter_pool_comm) to put all the segments of input 
across the nodes  into one output file.

When I run the modified QE code in parallel, the output file is different from 
the serial run.

Does the QE's mp_sum allow the above operation for a three-D array?

Any hints or suggestions would be greatly appreciated.

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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Re: [Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Hi Ye,

Thank you for your suggestion. I tried it and when I ran the code, it 
seg-faulted. I put flags in the code to see where the segmentation faults 
occurs. It happens as the code calls mp_sum. It seems that mp_sum may not
be able to handle this reduction.

Cheers,
Vahid

On Oct 28, 2016, at 2:51 PM, Ye Luo 
mailto:xw111lu...@gmail.com>> wrote:

In Fortran, whatever-D array is 1-D array. mp_sum should be fine.
I saw something strange in your code that you were not copying the right things 
as you expected.
How about the following?
output(1:3,1:nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(1:3,1:nbnds,1:k_pool)

Ye

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory

2016-10-28 12:29 GMT-05:00 Vahid Askarpour 
mailto:vh261...@dal.ca>>:
Dear QE Users,

I am working on some modifications to the QE-6.0 code using symmetry. When I 
try to combine a 3-D array scattered across nodes, I use the following:

output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(3,nbnds,1:k_pool)

Here, nbnds is the number of bands, k_pool is the number of k points/pool, and 
pool_id is the id of the pool. Here I am assuming the the number of k points is 
divisible by the number of pools.

Then I call mp_sum(output,inter_pool_comm) to put all the segments of input 
across the nodes  into one output file.

When I run the modified QE code in parallel, the output file is different from 
the serial run.

Does the QE's mp_sum allow the above operation for a three-D array?

Any hints or suggestions would be greatly appreciated.

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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[Pw_forum] Gathering 3-d arrays across pools using QE's mp_sum

[Vahid Askarpour]

Dear QE Users,

I am working on some modifications to the QE-6.0 code using symmetry. When I 
try to combine a 3-D array scattered across nodes, I use the following:

output(3,nbnds,(k_pool*pool_id+1:k_pool*pool_id+k_pool))=input(3,nbnds,1:k_pool)

Here, nbnds is the number of bands, k_pool is the number of k points/pool, and 
pool_id is the id of the pool. Here I am assuming the the number of k points is 
divisible by the number of pools.

Then I call mp_sum(output,inter_pool_comm) to put all the segments of input 
across the nodes  into one output file.

When I run the modified QE code in parallel, the output file is different from 
the serial run.

Does the QE's mp_sum allow the above operation for a three-D array?

Any hints or suggestions would be greatly appreciated.

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada
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