[Pw_forum] Problem in average.x
Giovanni Cantele
giovanni.cantele at spin.cnr.it
Wed Sep 23 09:45:18 CEST 2015
Try to relaunch it on just one processor, usually it is very fast and it does not require parallelization.
Giovanni
> On 23 Sep 2015, at 00:06, Huang, Xu <xu-huang at uiowa.edu> wrote:
>
> 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 <http://www.quantum-espresso.org/>",
> in publications or presentations arising from this work. More details at
> http://www.quantum-espresso.org/quote <http://www.quantum-espresso.org/quote>
>
> Parallel version (MPI), running on 16 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 $results
>
> cat > Fe2O3.scf.in <<EOF
> &CONTROL
> calculation = 'scf',
> pseudo_dir = '/Users/xhuang3/pwf/',
> outdir='$temp/',
> prefix = 'Fe2O3',
> /
> &SYSTEM
> ibrav = 4,
> celldm(1) = 9.536271655,
> celldm(3) = 6.000000000,
> nat = 30,
> ntyp = 3,
> ecutwfc = 35,
> ecutrho = 280,
> occupations = 'smearing',
> smearing = 'mp',
> degauss = 0.02,
> nspin = 2,
> starting_magnetization(1) = 0.5,
> starting_magnetization(2) = -0.5,
> /
> &ELECTRONS
> mixing_beta = 0.4,
> conv_thr = 1.0d-6,
> /
> ATOMIC_SPECIES
> Fe1 1.0 Fe.pbe-nd-rrkjus.UPF
> Fe2 1.0 Fe.pbe-nd-rrkjus.UPF
> O 1.0 O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {crystal}
> Fe1 0.333333330 0.333333330 0.019799034
> Fe2 0.666666670 0.000000000 0.060629428
> Fe2 0.000000000 0.666666670 0.075292861
> Fe1 0.333333330 0.333333330 0.135189943
> Fe1 0.666666670 0.000000000 0.155817104
> Fe2 0.000000000 0.666666670 0.210485936
> Fe2 0.333333330 0.333333330 0.232350369
> Fe1 0.666666670 0.000000000 0.287045648
> Fe1 0.000000000 0.666666670 0.307656149
> Fe2 0.333333330 0.333333330 0.367558597
> Fe2 0.666666670 0.000000000 0.382170005
> Fe1 0.000000000 0.666666670 0.423088504
> O -0.008926107 -0.020983988 0.031308650
> O 0.321275458 0.675592765 0.031308650
> O 0.687650647 0.345391225 0.031308650
> O -0.021172740 0.313345511 0.106625540
> O 0.667851616 0.687839421 0.106625540
> O 0.353321125 -0.001184934 0.106625540
> O 0.024534827 0.024970890 0.183306362
> O 0.333769369 0.642131830 0.183306362
> O 0.641695804 0.332897279 0.183306362
> O -0.000469120 0.357826954 0.259526509
> O 0.691629403 0.667135802 0.259526509
> O 0.308839717 -0.024962756 0.259526509
> O -0.019998485 0.001310105 0.336192461
> O 0.354641930 0.686665178 0.336192461
> O 0.665356554 0.312024717 0.336192461
> O 0.012004812 0.324454789 0.411508891
> O 0.645783306 0.654661835 0.411508891
> O 0.342211883 0.020883376 0.411508891
> K_POINTS (automatic)
> 4 4 1 1 1 1
> EOF
>
> mpirun -n 16 $BIN_DIR/pw.x < Fe2O3.scf.in > Fe2O3.scf.out
>
> cat > Fe2O3.pp.in <<EOF
> &inputpp
> prefix = 'Fe2O3'
> outdir='$temp/',
> filplot = 'Fe2O3.potential'
> plot_num = 1
> /
> EOF
>
> mpirun -n 16 $BIN_DIR/pp.x < Fe2O3.pp.in > Fe2O3.pp.out
>
> ### average calculation
> cat > Fe2O3.avg.in <<EOF
> 1
> Fe2O3.potential
> 1.0d0
> 480
> 3
> 4.000000
> EOF
>
> mpirun -n 16 $BIN_DIR/average.x < Fe2O3.avg.in > Fe2O3.avg.out
>
> mv Fe2O3.* $results/
>
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--
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.cantele at 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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