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Dear Julien,<br>
<br>
it's actually described indirectly in the paper - in all figures you
can see that the<br>
system is centered a z = 0. Otherwise, the cutoff will cut off some
of the real<br>
Coulomb interactions. Probably this should be added to the
description, but this<br>
should be done by the original author. If he doesn't answer here, I
will contact<br>
him.<br>
<br>
The way you center should be more like (zh+zl)=0 - I don't
understand why<br>
you want to divide by 2 (zero divided by 2?!). That the slab isn't
centered should<br>
not be problematic. From your input I also see that the vacuum
region should be<br>
large enough but maybe you can try increasing it a bit more - maybe
increase the<br>
cell dimension in z to 45 or 50 Angstrom?<br>
<br>
Cheerio<br>
<br>
Thomas<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/12/19 11:30 AM, JULIEN, CLAUDE,
PIERRE BARBAUD wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Well
actually, this remark may be much closer to solve my problem
than you might think !<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I
tried to run the simulation again on the cluster without the
assume_isolated=’2D’ flag, and the parallelization was
efficient this time. It seemed to scale well with growing
number of procs. So thank you very much for this suggestion.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However,
this raised other questions that I was not able to find an
answer to:<o:p></o:p></span></p>
<p class="MsoListParagraph"
style="text-indent:-18.0pt;mso-list:l1 level1 lfo2"><!--[if !supportLists]--><span
style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span
style="mso-list:Ignore">·<span style="font:7.0pt
"Times New Roman""> </span></span></span><!--[endif]--><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Where
does the information about the need to center the system
come from? I could not find track of it in the INPUT_PW
documentation. I only quickly glanced over the paper
mentioned as reference in the ‘2D’ flag, but I don’t suppose
that such technical details would be explained there ( as I
imagine that it is more relevant to the particular coding
implementation in quantum espresso than the general method
described in the article)<o:p></o:p></span></p>
<p class="MsoListParagraph"
style="text-indent:-18.0pt;mso-list:l1 level1 lfo2"><!--[if !supportLists]--><span
style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span
style="mso-list:Ignore">·<span style="font:7.0pt
"Times New Roman""> </span></span></span><!--[endif]--><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I
tried to correct the assume_isolated, but I might have
misunderstood how to center the system. I just took the atom
with “highest z” zh and the one with “lowest z” zl, and made
sure to shift the whole so that the average (zh+zl)/2=0.
This did not work. However, this particular example being
made of a slab and a 2d layer over it, this means, among
others, that the slab itself is not centered, and I am
unsure whether this is the correct way to do it<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Julien<o:p></o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext">
Thomas Brumme [<a class="moz-txt-link-freetext" href="mailto:thomas.brumme@uni-leipzig.de">mailto:thomas.brumme@uni-leipzig.de</a>] <br>
<b>Sent:</b> mercredi 10 avril 2019 18:19<br>
<b>To:</b> Quantum Espresso users Forum; Julien Barbaud<br>
<b>Subject:</b> Re: [QE-users] unefficient
parallelization of scf calculation<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Julien,<br>
<br>
I can't give any valuable input for your question regarding
the parallelization, but I think your<br>
input is wrong. Using assume_isolated needs the system to be
centered around z=0.<br>
<br>
Regards<br>
<br>
Thomas<o:p></o:p></p>
<div>
<p class="MsoNormal">On 4/10/19 11:36 AM, Julien Barbaud
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
am starting to use a hpc cluster of my university, but I am
very green on parallel computation.<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
have made a first test (test #1) on a very small-scale
simulation (relaxation of a GO sheet with 19 atoms, with
respect to the gamma point). The calculation took 3m20s to
run on 1 proc on my personal computer. On the cluster with 4
proc and default parallel options, it took 1m5s, and on 8
proc it took 44s. This seems like a reasonable behavior, and
at least shows that raising the number of procs does reduce
computation time in this case (with obvious limitations if
too many procs for the job).<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However
I tried with another test, a bit bigger (test #2). This
example is a scf calculation with 120 atoms (still with
respect to the gamma point). In this case, the
parallelization brings absolutely no improvement. In fact,
although the <i>outfile</i> confirms that the code is
running on N procs, it has similar performances as if it was
running on 1 proc (sometimes even worse actually, but
probably not in a significant manner, as the times are
fluctuating a bit from 1 run to another)<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
tried to run this same input file on my personal computer
both on 1 and 2 cores. Turns out that it takes 10376s to run
10 iterations on 1 core, while it takes 6777s on two cores,
so it seems that the parallelization is doing ok on my
computer.<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
have tried to run with different number of cores on the hpc,
and different parallelization options (like for instance –nb
4), but nothing seems to improve the time<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Basically,
I am stuck with those 2 seemingly conflicting facts:<o:p></o:p></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">Parallelization seems to have no particular
problem on the hpc cluster because test #1 gives good
results<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">Parallelization seems to have no particular
problem with the particular input file #2 because it seems
to scale reasonably with proc number on my individual
computer<o:p></o:p></li>
</ul>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However,
combining both and running this file in parallel on the hpc
cluster ends up not working correctly…<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
included below the input file and output file of test #2. I
also included as well as the slurm script that I use to
submit the calculation to the job manager, in case it helps
(test2.scf.slurm.txt)<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any
suggestion on what is going wrong would be very welcome.<o:p></o:p></p>
<p>Julien<o:p></o:p></p>
<p><o:p> </o:p></p>
<p><b><span style="font-size:18.0pt">----------------------------------test2.in---------------------------------------</span></b><o:p></o:p></p>
<p><o:p> </o:p></p>
<p style="margin-bottom:12.0pt">&CONTROL<br>
title = '# Quantum Espresso PWSCF output snapshot # 0'<br>
pseudo_dir =
'/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/' ,<br>
prefix='bonding_scf'<br>
calculation = 'scf'<br>
outdir='./outslurm'<br>
/<br>
<br>
&SYSTEM<br>
nat= 120<br>
ntyp= 7<br>
ibrav= 0<br>
ecutwfc= 50, ecutrho=400,<br>
occupations='smearing', smearing='mv', degauss=1.0d-3<br>
assume_isolated='2D'<br>
/<br>
<br>
&ELECTRONS<br>
mixing_beta = 0.5<br>
conv_thr = 1.0d-7<br>
electron_maxstep=1<br>
/<br>
<br>
&IONS<br>
/<br>
<br>
&CELL<br>
/<br>
<br>
ATOMIC_SPECIES<br>
C 12.011 C.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
N 14.007 N.pbesol-n-kjpaw_psl.0.1.UPF<br>
H 1.008 H.pbesol-kjpaw_psl.0.1.UPF<br>
Pb 207.2 Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF<br>
I 126.9 I.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
O 15.999 O.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
Cl 35.450 Cl.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
<br>
<br>
CELL_PARAMETERS angstrom<br>
6.40743642 0.00000000 0.00000000<br>
0.00000000 12.53119000 0.00000000<br>
0.00000000 0.00000000 39.01263233<br>
<br>
<br>
ATOMIC_POSITIONS angstrom<br>
C 3.20373698 3.26295456 22.67510117<br>
N 4.36830205 2.66824164 22.67510117<br>
N 2.03914607 2.66824164 22.67510117<br>
H 3.20373076 4.35970913 22.67510117<br>
H 5.20200492 3.26227865 22.67510117<br>
H 4.49794030 1.65118734 22.67510117<br>
H 1.90952027 1.65118734 22.67510117<br>
H 1.20545622 3.26227865 22.67510117<br>
Pb 6.40746106 6.04808537 19.50631617<br>
I 3.20373108 6.16571088 19.50631617<br>
I 6.40746051 2.89948619 19.50631617<br>
I 0.00000101 5.76270558 22.67510117<br>
C 3.20373698 9.52854956 22.67510117<br>
N 4.36830205 8.93383664 22.67510117<br>
N 2.03914607 8.93383664 22.67510117<br>
H 3.20373076 10.62530413 22.67510117<br>
H 5.20200492 9.52787365 22.67510117<br>
H 4.49794030 7.91678234 22.67510117<br>
H 1.90952027 7.91678234 22.67510117<br>
H 1.20545622 9.52787365 22.67510117<br>
Pb 6.40746106 12.31368037 19.50631617<br>
I 3.20373108 12.43130588 19.50631617<br>
I 6.40746051 9.16508119 19.50631617<br>
I 0.00000101 12.02830057 22.67510117<br>
C 3.20373698 3.26295456 29.01264528<br>
N 4.36830205 2.66824164 29.01264528<br>
N 2.03914607 2.66824164 29.01264528<br>
H 3.20373076 4.35970913 29.01264528<br>
H 5.20200492 3.26227865 29.01264528<br>
H 4.49794030 1.65118734 29.01264528<br>
H 1.90952027 1.65118734 29.01264528<br>
H 1.20545622 3.26227865 29.01264528<br>
Pb 6.40746106 6.04808537 25.84386028<br>
I 3.20373108 6.16571088 25.84386028<br>
I 6.40746051 2.89948619 25.84386028<br>
I 0.00000101 5.76270558 29.01264528<br>
C 3.20373698 9.52854956 29.01264528<br>
N 4.36830205 8.93383664 29.01264528<br>
N 2.03914607 8.93383664 29.01264528<br>
H 3.20373076 10.62530413 29.01264528<br>
H 5.20200492 9.52787365 29.01264528<br>
H 4.49794030 7.91678234 29.01264528<br>
H 1.90952027 7.91678234 29.01264528<br>
H 1.20545622 9.52787365 29.01264528<br>
Pb 6.40746106 12.31368037 25.84386028<br>
I 3.20373108 12.43130588 25.84386028<br>
I 6.40746051 9.16508119 25.84386028<br>
I 0.00000101 12.02830057 29.01264528<br>
C 3.20373698 3.26295456 35.35018939<br>
N 4.36830205 2.66824164 35.35018939<br>
N 2.03914607 2.66824164 35.35018939<br>
H 3.20373076 4.35970913 35.35018939<br>
H 5.20200492 3.26227865 35.35018939<br>
H 4.49794030 1.65118734 35.35018939<br>
H 1.90952027 1.65118734 35.35018939<br>
H 1.20545622 3.26227865 35.35018939<br>
Pb 6.40746106 6.04808537 32.18140439<br>
I 3.20373108 6.16571088 32.18140439<br>
I 6.40746051 2.89948619 32.18140439<br>
I 0.00000101 5.76270558 35.35018939<br>
C 3.20373698 9.52854956 35.35018939<br>
N 4.36830205 8.93383664 35.35018939<br>
N 2.03914607 8.93383664 35.35018939<br>
H 3.20373076 10.62530413 35.35018939<br>
H 5.20200492 9.52787365 35.35018939<br>
H 4.49794030 7.91678234 35.35018939<br>
H 1.90952027 7.91678234 35.35018939<br>
H 1.20545622 9.52787365 35.35018939<br>
Pb 6.40746106 12.31368037 32.18140439<br>
I 3.20373108 12.43130588 32.18140439<br>
I 6.40746051 9.16508119 32.18140439<br>
I 0.00000101 12.02830057 35.35018939<br>
C -2.65922562 1.02746622 13.15267801<br>
C -1.57082020 2.76789659 14.15213700<br>
C -1.55249267 1.43382279 13.92545145<br>
C -2.76678501 3.43396657 13.80880118<br>
C -0.51572401 0.59007742 14.27042957<br>
C 0.45127539 2.57771266 15.36479250<br>
C 0.54032636 1.13871696 14.89500427<br>
C -0.61858466 3.46111062 14.87552012<br>
C 1.75850840 0.45260751 14.42517077<br>
C 2.51877126 2.72823145 14.25997933<br>
C 2.54527275 1.46853929 13.80948684<br>
C 1.69149484 3.42061251 15.24764489<br>
C -2.84434923 4.73311498 13.75015587<br>
C -1.79251576 6.80155604 13.82062727<br>
C -1.71556103 5.46156288 14.02089871<br>
C -2.79591766 7.89012407 13.91075998<br>
C -0.67171524 4.85078215 14.72657807<br>
C 0.42299842 7.09269756 14.52980725<br>
C 0.31418038 5.75006370 15.32008815<br>
C -0.54822530 7.37927093 13.62065670<br>
C 1.58501883 4.93901110 15.15192558<br>
C 1.95672818 6.38683569 12.97082740<br>
C 2.39800998 5.48893963 14.08928384<br>
C 2.19010582 7.82391704 13.36789777<br>
C -2.58931431 9.73216977 11.12323260<br>
C -1.53736385 11.49261513 12.63531287<br>
C -1.43991415 10.25590370 11.85590265<br>
C -2.46212319 12.58463568 12.27360914<br>
C -0.60003148 9.34961386 12.41523759<br>
C 0.61521796 10.90977347 13.68739727<br>
C 0.56702168 9.72454135 13.05961564<br>
C -0.57311928 11.74387481 13.77090253<br>
C 1.73778864 8.96596466 12.44952664<br>
C 2.44039831 11.26999757 12.43362532<br>
C 2.66220529 10.00525725 12.01318349<br>
C 1.83430055 11.66382030 13.76046404<br>
Cl -0.00001799 6.04797424 17.07363791<br>
Cl 1.25165378 8.40223027 10.76754187<br>
O -1.79125675 11.13196776 14.04477237<br>
O 2.87346590 12.19705486 11.50562577<br>
O 2.66595523 5.77705032 15.51329335<br>
O 1.68196546 5.86106544 11.91469705<br>
O 2.44111071 11.89613785 15.06748010<br>
O 3.89019144 8.86144083 14.58391140<br>
O -2.48663871 8.96018517 10.18744705<br>
O -0.74483722 7.99628057 12.39035840<br>
O 1.51084248 7.88917390 14.66305294<br>
O 1.28942315 2.85893197 16.48674549<br>
<br>
<br>
K_POINTS gamma<o:p></o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p><b><span style="font-size:18.0pt">-----------------------------------------------------test2.out--------------------------------------------</span></b><o:p></o:p></p>
<p><o:p> </o:p></p>
<p><br>
Program PWSCF v.6.3 starts on 10Apr2019 at 15:35:34 <br>
<br>
This program is part of the open-source Quantum
ESPRESSO suite<br>
for quantum simulation of materials; please cite<br>
"P. Giannozzi et al., J. Phys.:Condens. Matter 21
395502 (2009);<br>
"P. Giannozzi et al., J. Phys.:Condens. Matter 29
465901 (2017);<br>
URL <a href="http://www.quantum-espresso.org"
moz-do-not-send="true">http://www.quantum-espresso.org</a>",
<br>
in publications or presentations arising from this
work. More details at<br>
<a href="http://www.quantum-espresso.org/quote"
moz-do-not-send="true">http://www.quantum-espresso.org/quote</a><br>
<br>
Parallel version (MPI), running on 8 processors<br>
<br>
MPI processes distributed on 1 nodes<br>
R & G space division: proc/nbgrp/npool/nimage
= 8<br>
Reading input from
/lustre/home/acct-mseyxd/mseyxd/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in<br>
Warning: card &IONS ignored<br>
Warning: card / ignored<br>
Warning: card &CELL ignored<br>
Warning: card / ignored<br>
<br>
Current dimensions of program PWSCF are:<br>
Max number of different atomic species (ntypx) = 10<br>
Max number of k-points (npk) = 40000<br>
Max angular momentum in pseudopotentials (lmaxx) = 3<br>
file C.pbesol-n-kjpaw_psl.1.0.0.UPF:
wavefunction(s) 2S 2P renormalized<br>
file N.pbesol-n-kjpaw_psl.0.1.UPF:
wavefunction(s) 2P renormalized<br>
file H.pbesol-kjpaw_psl.0.1.UPF:
wavefunction(s) 1S renormalized<br>
file Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF:
wavefunction(s) 6S 6P 5D renormalized<br>
file I.pbesol-n-kjpaw_psl.1.0.0.UPF:
wavefunction(s) 5S renormalized<br>
file O.pbesol-n-kjpaw_psl.1.0.0.UPF:
wavefunction(s) 2S 2P renormalized<br>
file Cl.pbesol-n-kjpaw_psl.1.0.0.UPF:
wavefunction(s) 3S 3P renormalized<br>
<br>
gamma-point specific algorithms are used<br>
<br>
Subspace diagonalization in iterative solution of the
eigenvalue problem:<br>
a serial algorithm will be used<br>
<br>
<br>
Parallelization info<br>
--------------------<br>
sticks: dense smooth PW G-vecs: dense
smooth PW<br>
Min 1140 570 141 356988
126222 15758<br>
Max 1142 572 142 357012
126236 15798<br>
Sum 9123 4565 1135 2856023
1009807 126259<br>
<br>
<br>
Title: <br>
# Quantum Espresso PWSCF output snapshot #
0 <br>
<br>
<br>
bravais-lattice index = 0<br>
lattice parameter (alat) = 12.1083 a.u.<br>
unit-cell volume = 21138.7101 (a.u.)^3<br>
number of atoms/cell = 120<br>
number of atomic types = 7<br>
number of electrons = 542.00<br>
number of Kohn-Sham states= 325<br>
kinetic-energy cutoff = 50.0000 Ry<br>
charge density cutoff = 400.0000 Ry<br>
convergence threshold = 1.0E-07<br>
mixing beta = 0.5000<br>
number of iterations used = 8 plain
mixing<br>
Exchange-correlation = SLA PW PSX PSC ( 1 4 10 8
0 0)<br>
<br>
celldm(1)= 12.108300 celldm(2)= 0.000000
celldm(3)= 0.000000<br>
celldm(4)= 0.000000 celldm(5)= 0.000000
celldm(6)= 0.000000<br>
<br>
crystal axes: (cart. coord. in units of alat)<br>
a(1) = ( 1.000000 0.000000 0.000000 )
<br>
a(2) = ( 0.000000 1.955726 0.000000 )
<br>
a(3) = ( 0.000000 0.000000 6.088649 )
<br>
<br>
reciprocal axes: (cart. coord. in units 2 pi/alat)<br>
b(1) = ( 1.000000 0.000000 0.000000 ) <br>
b(2) = ( 0.000000 0.511319 0.000000 ) <br>
b(3) = ( 0.000000 0.000000 0.164240 ) <br>
<br>
<br>
PseudoPot. # 1 for C read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/C.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
MD5 check sum: f9b2fe17d1f478429498b05d17159f9e<br>
Pseudo is Projector augmented-wave + core cor, Zval =
4.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1073 points, 4 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 2 for N read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/N.pbesol-n-kjpaw_psl.0.1.UPF<br>
MD5 check sum: 15bd223d5d75e9eda893d0f4e6bdad1b<br>
Pseudo is Projector augmented-wave + core cor, Zval =
5.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1085 points, 4 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 3 for H read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/H.pbesol-kjpaw_psl.0.1.UPF<br>
MD5 check sum: 27a6b98f1514c59d399e798f1258b8b7<br>
Pseudo is Projector augmented-wave, Zval = 1.0<br>
Generated using "atomic" code by A. Dal Corso v.5.0.2
svn rev. 9415<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 929 points, 2 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 4 for Pb read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF<br>
MD5 check sum: 56da3be0db09ba43f309b470f7bff7d1<br>
Pseudo is Projector augmented-wave + core cor, Zval =
14.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1281 points, 6 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
l(5) = 2<br>
l(6) = 2<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 5 for I read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/I.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
MD5 check sum: 6038403ff9b03366b27f71806436e734<br>
Pseudo is Projector augmented-wave + core cor, Zval =
7.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1247 points, 6 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
l(5) = 2<br>
l(6) = 2<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 6 for O read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/O.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
MD5 check sum: cb766521a97cf798d01896eaf7ac9a0a<br>
Pseudo is Projector augmented-wave + core cor, Zval =
6.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1095 points, 4 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
PseudoPot. # 7 for Cl read from file:<br>
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Cl.pbesol-n-kjpaw_psl.1.0.0.UPF<br>
MD5 check sum: 939a64fc035742408689cdf8470f8314<br>
Pseudo is Projector augmented-wave + core cor, Zval =
7.0<br>
Generated using "atomic" code by A. Dal Corso v.6.3<br>
Shape of augmentation charge: PSQ<br>
Using radial grid of 1157 points, 6 beta functions
with: <br>
l(1) = 0<br>
l(2) = 0<br>
l(3) = 1<br>
l(4) = 1<br>
l(5) = 2<br>
l(6) = 2<br>
Q(r) pseudized with 0 coefficients <br>
<br>
<br>
atomic species valence mass pseudopotential<br>
C 4.00 12.01100 C ( 1.00)<br>
N 5.00 14.00700 N ( 1.00)<br>
H 1.00 1.00800 H ( 1.00)<br>
Pb 14.00 207.20000 Pb( 1.00)<br>
I 7.00 126.90000 I ( 1.00)<br>
O 6.00 15.99900 O ( 1.00)<br>
Cl 7.00 35.45000 Cl( 1.00)<br>
<br>
No symmetry found<br>
<br>
<br>
<br>
Cartesian axes<br>
<br>
site n. atom positions (alat
units)<br>
1 C tau( 1) = ( 0.5000029
0.5092449 3.5388726 )<br>
2 N tau( 2) = ( 0.6817550
0.4164289 3.5388726 )<br>
3 N tau( 3) = ( 0.3182468
0.4164289 3.5388726 )<br>
4 H tau( 4) = ( 0.5000020
0.6804140 3.5388726 )<br>
5 H tau( 5) = ( 0.8118699
0.5091394 3.5388726 )<br>
6 H tau( 6) = ( 0.7019875
0.2576986 3.5388726 )<br>
7 H tau( 7) = ( 0.2980163
0.2576986 3.5388726 )<br>
8 H tau( 8) = ( 0.1881339
0.5091394 3.5388726 )<br>
9 Pb tau( 9) = ( 1.0000038
0.9439166 3.0443246 )<br>
10 I tau( 10) = ( 0.5000020
0.9622742 3.0443246 )<br>
11 I tau( 11) = ( 1.0000038
0.4525189 3.0443246 )<br>
12 I tau( 12) = ( 0.0000002
0.8993777 3.5388726 )<br>
13 C tau( 13) = ( 0.5000029
1.4871079 3.5388726 )<br>
14 N tau( 14) = ( 0.6817550
1.3942919 3.5388726 )<br>
15 N tau( 15) = ( 0.3182468
1.3942919 3.5388726 )<br>
16 H tau( 16) = ( 0.5000020
1.6582770 3.5388726 )<br>
17 H tau( 17) = ( 0.8118699
1.4870024 3.5388726 )<br>
18 H tau( 18) = ( 0.7019875
1.2355616 3.5388726 )<br>
19 H tau( 19) = ( 0.2980163
1.2355616 3.5388726 )<br>
20 H tau( 20) = ( 0.1881339
1.4870024 3.5388726 )<br>
21 Pb tau( 21) = ( 1.0000038
1.9217796 3.0443246 )<br>
22 I tau( 22) = ( 0.5000020
1.9401372 3.0443246 )<br>
23 I tau( 23) = ( 1.0000038
1.4303819 3.0443246 )<br>
24 I tau( 24) = ( 0.0000002
1.8772407 3.5388726 )<br>
25 C tau( 25) = ( 0.5000029
0.5092449 4.5279646 )<br>
26 N tau( 26) = ( 0.6817550
0.4164289 4.5279646 )<br>
27 N tau( 27) = ( 0.3182468
0.4164289 4.5279646 )<br>
28 H tau( 28) = ( 0.5000020
0.6804140 4.5279646 )<br>
29 H tau( 29) = ( 0.8118699
0.5091394 4.5279646 )<br>
30 H tau( 30) = ( 0.7019875
0.2576986 4.5279646 )<br>
31 H tau( 31) = ( 0.2980163
0.2576986 4.5279646 )<br>
32 H tau( 32) = ( 0.1881339
0.5091394 4.5279646 )<br>
33 Pb tau( 33) = ( 1.0000038
0.9439166 4.0334166 )<br>
34 I tau( 34) = ( 0.5000020
0.9622742 4.0334166 )<br>
35 I tau( 35) = ( 1.0000038
0.4525189 4.0334166 )<br>
36 I tau( 36) = ( 0.0000002
0.8993777 4.5279646 )<br>
37 C tau( 37) = ( 0.5000029
1.4871079 4.5279646 )<br>
38 N tau( 38) = ( 0.6817550
1.3942919 4.5279646 )<br>
39 N tau( 39) = ( 0.3182468
1.3942919 4.5279646 )<br>
40 H tau( 40) = ( 0.5000020
1.6582770 4.5279646 )<br>
41 H tau( 41) = ( 0.8118699
1.4870024 4.5279646 )<br>
42 H tau( 42) = ( 0.7019875
1.2355616 4.5279646 )<br>
43 H tau( 43) = ( 0.2980163
1.2355616 4.5279646 )<br>
44 H tau( 44) = ( 0.1881339
1.4870024 4.5279646 )<br>
45 Pb tau( 45) = ( 1.0000038
1.9217796 4.0334166 )<br>
46 I tau( 46) = ( 0.5000020
1.9401372 4.0334166 )<br>
47 I tau( 47) = ( 1.0000038
1.4303819 4.0334166 )<br>
48 I tau( 48) = ( 0.0000002
1.8772407 4.5279646 )<br>
49 C tau( 49) = ( 0.5000029
0.5092449 5.5170566 )<br>
50 N tau( 50) = ( 0.6817550
0.4164289 5.5170566 )<br>
51 N tau( 51) = ( 0.3182468
0.4164289 5.5170566 )<br>
52 H tau( 52) = ( 0.5000020
0.6804140 5.5170566 )<br>
53 H tau( 53) = ( 0.8118699
0.5091394 5.5170566 )<br>
54 H tau( 54) = ( 0.7019875
0.2576986 5.5170566 )<br>
55 H tau( 55) = ( 0.2980163
0.2576986 5.5170566 )<br>
56 H tau( 56) = ( 0.1881339
0.5091394 5.5170566 )<br>
57 Pb tau( 57) = ( 1.0000038
0.9439166 5.0225086 )<br>
58 I tau( 58) = ( 0.5000020
0.9622742 5.0225086 )<br>
59 I tau( 59) = ( 1.0000038
0.4525189 5.0225086 )<br>
60 I tau( 60) = ( 0.0000002
0.8993777 5.5170566 )<br>
61 C tau( 61) = ( 0.5000029
1.4871079 5.5170566 )<br>
62 N tau( 62) = ( 0.6817550
1.3942919 5.5170566 )<br>
63 N tau( 63) = ( 0.3182468
1.3942919 5.5170566 )<br>
64 H tau( 64) = ( 0.5000020
1.6582770 5.5170566 )<br>
65 H tau( 65) = ( 0.8118699
1.4870024 5.5170566 )<br>
66 H tau( 66) = ( 0.7019875
1.2355616 5.5170566 )<br>
67 H tau( 67) = ( 0.2980163
1.2355616 5.5170566 )<br>
68 H tau( 68) = ( 0.1881339
1.4870024 5.5170566 )<br>
69 Pb tau( 69) = ( 1.0000038
1.9217796 5.0225086 )<br>
70 I tau( 70) = ( 0.5000020
1.9401372 5.0225086 )<br>
71 I tau( 71) = ( 1.0000038
1.4303819 5.0225086 )<br>
72 I tau( 72) = ( 0.0000002
1.8772407 5.5170566 )<br>
73 C tau( 73) = ( -0.4150218
0.1603553 2.0527208 )<br>
74 C tau( 74) = ( -0.2451558
0.4319819 2.2087050 )<br>
75 C tau( 75) = ( -0.2422954
0.2237748 2.1733265 )<br>
76 C tau( 76) = ( -0.4318084
0.5359346 2.1551211 )<br>
77 C tau( 77) = ( -0.0804884
0.0920926 2.2271668 )<br>
78 C tau( 78) = ( 0.0704299
0.4023002 2.3979625 )<br>
79 C tau( 79) = ( 0.0843280
0.1777180 2.3246433 )<br>
80 C tau( 80) = ( -0.0965417
0.5401709 2.3216025 )<br>
81 C tau( 81) = ( 0.2744480
0.0706378 2.2513170 )<br>
82 C tau( 82) = ( 0.3931012
0.4257914 2.2255358 )<br>
83 C tau( 83) = ( 0.3972373
0.2291930 2.1552281 )<br>
84 C tau( 84) = ( 0.2639893
0.5338504 2.3796795 )<br>
85 C tau( 85) = ( -0.4439138
0.7386909 2.1459684 )<br>
86 C tau( 86) = ( -0.2797555
1.0615097 2.1569667 )<br>
87 C tau( 87) = ( -0.2677453
0.8523788 2.1882228 )<br>
88 C tau( 88) = ( -0.4363551
1.2314011 2.1710336 )<br>
89 C tau( 89) = ( -0.1048337
0.7570551 2.2983573 )<br>
90 C tau( 90) = ( 0.0660168
1.1069478 2.2676475 )<br>
91 C tau( 91) = ( 0.0490337
0.8974047 2.3909856 )<br>
92 C tau( 92) = ( -0.0855608
1.1516729 2.1257576 )<br>
93 C tau( 93) = ( 0.2473718
0.7708248 2.3647407 )<br>
94 C tau( 94) = ( 0.3053839
0.9967849 2.0243396 )<br>
95 C tau( 95) = ( 0.3742542
0.8566514 2.1988956 )<br>
96 C tau( 96) = ( 0.3418069
1.2210682 2.0863099 )<br>
97 C tau( 97) = ( -0.4041108
1.5188867 1.7359880 )<br>
98 C tau( 98) = ( -0.2399343
1.7936370 1.9719763 )<br>
99 C tau( 99) = ( -0.2247255
1.6006251 1.8503348 )<br>
100 C tau( 100) = ( -0.3842603
1.9640672 1.9155257 )<br>
101 C tau( 101) = ( -0.0936461
1.4591817 1.9376295 )<br>
102 C tau( 102) = ( 0.0960162
1.7026737 2.1361737 )<br>
103 C tau( 103) = ( 0.0884943
1.5176961 2.0381967 )<br>
104 C tau( 104) = ( -0.0894460
1.8328508 2.1492063 )<br>
105 C tau( 105) = ( 0.2712143
1.3993061 1.9429809 )<br>
106 C tau( 106) = ( 0.3808697
1.7588934 1.9404992 )<br>
107 C tau( 107) = ( 0.4154868
1.5615071 1.8748814 )<br>
108 C tau( 108) = ( 0.2862768
1.8203568 2.1475771 )<br>
109 Cl tau( 109) = ( -0.0000028
0.9438992 2.6646597 )<br>
110 Cl tau( 110) = ( 0.1953439
1.3113248 1.6804758 )<br>
111 O tau( 111) = ( -0.2795590
1.7373513 2.1919488 )<br>
112 O tau( 112) = ( 0.4484580
1.9035780 1.7956676 )<br>
113 O tau( 113) = ( 0.4160721
0.9016165 2.4211389 )<br>
114 O tau( 114) = ( 0.2625021
0.9147286 1.8595108 )<br>
115 O tau( 115) = ( 0.3809809
1.8566143 2.3515614 )<br>
116 O tau( 116) = ( 0.6071370
1.3829932 2.2760915 )<br>
117 O tau( 117) = ( -0.3880864
1.3984041 1.5899412 )<br>
118 O tau( 118) = ( -0.1162457
1.2479688 1.9337466 )<br>
119 O tau( 119) = ( 0.2357952
1.2312528 2.2884430 )<br>
120 O tau( 120) = ( 0.2012385
0.4461897 2.5730642 )<br>
<br>
number of k points= 1 Marzari-Vanderbilt smearing,
width (Ry)= 0.0010<br>
cart. coord. in units 2pi/alat<br>
k( 1) = ( 0.0000000 0.0000000 0.0000000),
wk = 2.0000000<br>
<br>
Dense grid: 1428012 G-vectors FFT dimensions: (
80, 160, 480)<br>
<br>
Smooth grid: 504904 G-vectors FFT dimensions: (
60, 108, 360)<br>
<br>
Estimated max dynamical RAM per process > 965.66
MB<br>
<br>
Estimated total dynamical RAM > 7.54 GB<br>
----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D<br>
The code is running with the 2D cutoff<br>
Please refer to:<br>
Sohier, T., Calandra, M., & Mauri, F. (2017), <br>
Density functional perturbation theory for gated
two-dimensional heterostructures:<br>
Theoretical developments and application to flexural
phonons in graphene.<br>
Physical Review B, 96(7), 75448. <a
href="https://doi.org/10.1103/PhysRevB.96.075448"
moz-do-not-send="true">https://doi.org/10.1103/PhysRevB.96.075448</a><br>
----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D<br>
<br>
Check: negative/imaginary core charge= -0.000002
0.000000<br>
<br>
Initial potential from superposition of free atoms<br>
Check: negative starting charge= -0.001132<br>
<br>
starting charge 541.98383, renormalised to 542.00000<br>
<br>
negative rho (up, down): 1.132E-03 0.000E+00<br>
Starting wfcs are 420 randomized atomic wfcs<br>
Checking if some PAW data can be deallocated... <br>
<br>
total cpu time spent up to now is 125.6 secs<br>
<br>
Self-consistent Calculation<br>
<br>
iteration # 1 ecut= 50.00 Ry beta= 0.50<br>
Davidson diagonalization with overlap<br>
c_bands: 3 eigenvalues not converged<br>
ethr = 1.00E-02, avg # of iterations = 40.0<br>
<br>
negative rho (up, down): 1.031E-05 0.000E+00<br>
<br>
total cpu time spent up to now is 2094.5 secs<br>
<br>
total energy = 82142.85683667 Ry<br>
Harris-Foulkes estimate = -53335.51769720 Ry<br>
estimated scf accuracy < 111068.31785845 Ry<br>
<br>
End of self-consistent calculation<br>
<br>
convergence NOT achieved after 1 iterations: stopping<br>
<br>
Writing output data file bonding_scf.save/<br>
<br>
init_run : 119.18s CPU 120.33s WALL ( 1
calls)<br>
electrons : 1961.71s CPU 1969.12s WALL ( 1
calls)<br>
<br>
Called by init_run:<br>
wfcinit : 52.26s CPU 52.44s WALL ( 1
calls)<br>
potinit : 19.26s CPU 19.33s WALL ( 1
calls)<br>
hinit0 : 36.63s CPU 36.68s WALL ( 1
calls)<br>
<br>
Called by electrons:<br>
c_bands : 1919.78s CPU 1923.97s WALL ( 1
calls)<br>
sum_band : 28.22s CPU 30.08s WALL ( 1
calls)<br>
v_of_rho : 2.26s CPU 2.35s WALL ( 2
calls)<br>
newd : 20.58s CPU 22.50s WALL ( 2
calls)<br>
PAW_pot : 4.00s CPU 4.00s WALL ( 2
calls)<br>
mix_rho : 0.23s CPU 0.24s WALL ( 1
calls)<br>
<br>
Called by c_bands:<br>
init_us_2 : 0.22s CPU 0.27s WALL ( 3
calls)<br>
regterg : 1919.41s CPU 1923.60s WALL ( 2
calls)<br>
<br>
Called by sum_band:<br>
sum_band:bec : 0.00s CPU 0.00s WALL ( 1
calls)<br>
addusdens : 16.57s CPU 17.94s WALL ( 1
calls)<br>
<br>
Called by *egterg:<br>
h_psi : 680.38s CPU 682.69s WALL ( 43
calls)<br>
s_psi : 259.57s CPU 259.75s WALL ( 43
calls)<br>
g_psi : 0.93s CPU 0.94s WALL ( 40
calls)<br>
rdiaghg : 52.76s CPU 52.86s WALL ( 41
calls)<br>
<br>
Called by h_psi:<br>
h_psi:pot : 679.62s CPU 681.90s WALL ( 43
calls)<br>
h_psi:calbec : 255.27s CPU 255.54s WALL ( 43
calls)<br>
vloc_psi : 164.42s CPU 166.01s WALL ( 43
calls)<br>
add_vuspsi : 259.93s CPU 260.35s WALL ( 43
calls)<br>
<br>
General routines<br>
calbec : 263.20s CPU 263.88s WALL ( 44
calls)<br>
fft : 2.33s CPU 2.43s WALL ( 23
calls)<br>
ffts : 0.09s CPU 0.09s WALL ( 3
calls)<br>
fftw : 128.50s CPU 130.07s WALL ( 10237
calls)<br>
interpolate : 0.25s CPU 0.26s WALL ( 2
calls)<br>
davcio : 0.00s CPU 0.10s WALL ( 3
calls)<br>
<br>
Parallel routines<br>
fft_scatt_xy : 23.50s CPU 23.55s WALL ( 10263
calls)<br>
fft_scatt_yz : 10.98s CPU 12.22s WALL ( 10263
calls)<br>
<br>
PWSCF : 34m45.53s CPU 34m55.12s WALL<br>
<br>
<br>
This run was terminated on: 16:10:30
10Apr2019 <br>
<br>
=------------------------------------------------------------------------------=<br>
JOB DONE.<br>
=------------------------------------------------------------------------------=<o:p></o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p><o:p> </o:p></p>
<p><b><span style="font-size:13.5pt">-----------------------------------------------------SLURM
command-------------------------------------</span></b><o:p></o:p></p>
<p><o:p> </o:p></p>
<p style="margin-bottom:12.0pt">#!/bin/bash<br>
<br>
#SBATCH --job-name=QE_GO-Cl_bonding_scf<br>
#SBATCH --partition=cpu<br>
#SBATCH --mail-type=end<br>
#SBATCH <a
href="mailto:--mail-user=julien_barbaud@sjtu.edu.cn"
moz-do-not-send="true">--mail-user=julien_barbaud@sjtu.edu.cn</a><br>
#SBATCH --output=bonding.scf.slurm.out<br>
#SBATCH --error=bonding.scf.slurm.err<br>
#SBATCH -p cpu<br>
#SBATCH -n 8 <br>
#SBATCH --ntasks-per-node=8<br>
<br>
ulimit -l unlimited<br>
ulimit -s unlimited<br>
<br>
INPUT=$HOME/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in<br>
EXEC=$HOME/QE/qe-6.3/bin/pw.x<br>
<br>
srun --mpi=pmi2 $EXEC -in $INPUT <o:p></o:p></p>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>users mailing list<o:p></o:p></pre>
<pre><a href="mailto:users@lists.quantum-espresso.org" moz-do-not-send="true">users@lists.quantum-espresso.org</a><o:p></o:p></pre>
<pre><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Dr. rer. nat. Thomas Brumme<o:p></o:p></pre>
<pre>Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry<o:p></o:p></pre>
<pre>Leipzig University<o:p></o:p></pre>
<pre>Phillipp-Rosenthal-Strasse 31<o:p></o:p></pre>
<pre>04103 Leipzig<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Tel: +49 (0)341 97 36456<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>email: <a href="mailto:thomas.brumme@uni-leipzig.de" moz-do-not-send="true">thomas.brumme@uni-leipzig.de</a><o:p></o:p></pre>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig
Tel: +49 (0)341 97 36456
email: <a class="moz-txt-link-abbreviated" href="mailto:thomas.brumme@uni-leipzig.de">thomas.brumme@uni-leipzig.de</a>
</pre>
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