[Pw_forum] Problem in average.x
Huang, Xu
xu-huang at uiowa.edu
Wed Sep 23 17:45:40 CEST 2015
I changed the ppn down to 1 and restart the last part. It's successful and finished just in a few seconds. Thank you very much!
Xu Huang
________________________________
From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of Giovanni Cantele [giovanni.cantele at spin.cnr.it]
Sent: Wednesday, September 23, 2015 2:45 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Problem in average.x
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<mailto: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
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<mailto: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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