[Pw_forum] Problem in average.x

[Huang, Xu]

Dear all,

I'm using QE to plot the layer-averaged potential for hematite (Fe2O3) surface 
slabs. I did scf (pw.x) first, then got the potential (pp.x), and finally tried 
to make layer-averaged potential (average.x) along surface normal. The first 2 
steps were successful and finished in ~10 minutes. But in the last step, the 
output file of average.x just stopped at the beginning for several days without 
any new update like this:
--
 Program AVERAGE v.5.1.1 starts on 20Sep2015 at 16:58:27

 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;,
 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
 Reading header from file  Fe2O3.potential

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1s, nr2s, nr3s values from input
--

And currently the all the files in the working directory are:
   2779 Sep 20 16:48 QEneonscript_pot_avg
2 Sep 20 16:49 results
   2150 Sep 20 16:49 Fe2O3.scf.in
   19 Sep 20 16:58 temp
127237 Sep 20 16:58 Fe2O3.scf.out
 138 Sep 20 16:58 Fe2O3.pp.in
 16051771 Sep 20 16:58 Fe2O3.potential
2263 Sep 20 16:58 Fe2O3.pp.out
39 Sep 20 16:58 Fe2O3.avg.in
  696 Sep 20 16:59 Fe2O3.avg.out

I'm very confused about it. I don't know if I missed anything in the script for 
the last step. Here I added the entire run script (QEneonscript_pot_avg) of 
this calculation with all 3 steps below. Thank you very much for helping me 
with this!

Regards,
Xu Huang

Below is the QEneonscript_pot_avg file:
---
#!/bin/bash
#$ -S /bin/bash
#$ -N uhv_pot
#$ -cwd
#$ -q UI
#$ -l std_mem
#$ -pe 16cpn 16

module load espresso/5.1.1
BIN_DIR=/opt/quantum-espresso/5.1.1/

temp=$PWD/temp
mkdir -p $temp

results=$PWD/results
mkdir -p $results

cat > Fe2O3.scf.in < Fe2O3.scf.out

cat > Fe2O3.pp.in < Fe2O3.pp.out

### average calculation
cat > Fe2O3.avg.in < Fe2O3.avg.out

mv Fe2O3.* $results/

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Re: [Pw_forum] Force calculation time in relaxation under electric field

[Mostafa Youssef]

The last time report I quoted is with Hubbard U and this in fact what I 
typically find in PWscf relaxation calculation.

I will send you the two output files offline. Thank you very much for your help!


Regards,
Mostafa
MIT
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Re: [Pw_forum] band parallelization

[Lorenzo Paulatto]

On Tuesday, September 22, 2015 10:42:13 AM Tiana Davide wrote:
> 
> is the principle correct or it should be done in another way?


Yes, but as the calculation is becoming slower with more CPU it means that 
communication is becoming too expensive. You have to check at the end of the 
output file to see what scales and what does not, in you case it is probably 
the Fourier transform that is killing you scaling, you can try to use some 
task groups (-ntg XX if I remember correctly) to see if you can scale a bit 
higher.

HTH

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

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Re: [Pw_forum] Reconstruction of Si 001 surface

[Giovanni Cantele]

Dear Bipul,

you are not actually doing a vc-relax calculation, because in your input 
calculation=relax. However, this is exactly what I would do, at least to start 
(for example, for a vc-relax calculation I guess that pw.x will try also to 
optimise the cell size along the z direction, where the dimension must be fixed 
according to the amount of vacuum you want to use).

In order to get the 2x1 reconstruction you should slightly move (with respect 
to their bulk positions) the two atoms expected to form a dimer along the 
proper direction. Otherwise, pw.x will find more symmetry than that of the 2x1 
reconstruction of the Si 001 surface, and will keep that symmetry during the 
whole calculation. Consider that, if you try to visualise the structure using 
XCrysDen, it seems that you are using a supercell larger than the minimal one 
needed to simulate that surface (I see two “dimers” within your supercell, so 
with that supercell you can also simulate the 2x2 reconstruction). The easiest 
way to get the minimal cell is to rotate, as far as I remember, the atoms by 45 
degrees in the x-y plane (around the z axis), so that the dimer gets parallel 
to, let’s say, the y direction. In this way it is also sufficient to replicate 
that supercell along x and y to get also 2x2 or 4x2 reconstructions.

Finally, you should check whether using an asymmetric slab model (because you 
fix the bottom layers of the slab) induces artificial dipole that must be 
corrected using dipfield and related variables in the input files.

Hope this helps.

Giovanni


> On 22 Sep 2015, at 12:12, Bipul Rakshit  wrote:
> 
> Dear Pwscf users,
> I want to study the Si 001 surface reconstruction. I am sending the input of 
> 2x1 Si (001) surface. I used 16 Ang Vaccuum between the slabs along 
> z-direction. I am using calculation = 'relax'. In the literature i find that 
> 2x1 reconstruction for Si (001) surface is there. But with the supplied input 
> after running the calculation, I am not getting the dimers which is expected 
> to form in 2x1 reconstruction.
> 
> I do use calculation=vc-relax, but the calculation is not converging after 
> 100 iterations and get killed.
> So what changes I have to made in the input so that i can get the 2x1 dimer 
> formation in the reconstructed surface.
> 
> kindly help me in this regard.
> 
> -- 
> Dr. Bipul Rakshit
> Research Associate,
> Institute of Physics (IOP),
> Bhubaneswar- 751 005
> Orissa 
> India
> <2x1-vc-relax.in>___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele



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[Pw_forum] band parallelization

[Tiana Davide]

Dear Lorenzo and Paolo

Sorry if I was not clear. 
I didn't know about the only hybrid calculation. This means my test is useless. 
Since I will use on hybrid I would like to check if my approach is correct of 
it I am doing something wrong.

What I was trying to say is that I run a gamma point calculation with 272 
orbitals. 
I run 3 tests using 

272 cores no band parallelisation
 Parallel version (MPI & OpenMP), running on 272 processor cores
 Number of MPI processes:   272
 Threads/MPI process: 1
 R & G space division:  proc/nbgrp/npool/nimage = 272

time for scf 2 cycles
 total cpu time spent up to now is   11.8 secs
 total cpu time spent up to now is   22.0 secs
 total cpu time spent up to now is   28.0 secs


544 cores using band parallelisation and 
 Parallel version (MPI & OpenMP), running on 544 processor cores
 Number of MPI processes:   544
 Threads/MPI process: 1
 band groups division:  nbgrp =   2
 R & G space division:  proc/nbgrp/npool/nimage = 272

time for scf 2 cycles
 total cpu time spent up to now is   15.1 secs
 total cpu time spent up to now is   27.3 secs
 total cpu time spent up to now is   33.9 secs

816 cores with 
 Parallel version (MPI & OpenMP), running on 816 processor cores
 Number of MPI processes:   816
 Threads/MPI process: 1
 band groups division:  nbgrp =   3
 R & G space division:  proc/nbgrp/npool/nimage = 272

time for 2 scf cycles
 total cpu time spent up to now is   20.5 secs
 total cpu time spent up to now is   30.4 secs
 total cpu time spent up to now is   36.5 secs

is the principle correct or it should be done in another way?

Many thanks
Davide



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[Pw_forum] Reconstruction of Si 001 surface

[Bipul Rakshit]

Dear Pwscf users,
I want to study the Si 001 surface reconstruction. I am sending the input
of 2x1 Si (001) surface. I used 16 Ang Vaccuum between the slabs along
z-direction. I am using calculation = 'relax'. In the literature i find
that 2x1 reconstruction for Si (001) surface is there. But with the
supplied input after running the calculation, I am not getting the dimers
which is expected to form in 2x1 reconstruction.

I do use calculation=vc-relax, but the calculation is not converging after
100 iterations and get killed.
So what changes I have to made in the input so that i can get the 2x1 dimer
formation in the reconstructed surface.

kindly help me in this regard.

-- 
Dr. Bipul Rakshit
Research Associate,
Institute of Physics (IOP),
Bhubaneswar- 751 005
Orissa
India


2x1-vc-relax.in
Description: Binary data
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