[QE-users] How to carry out a series of simulations at the same time and output the stress and energy to one file?

[Minho Lee]

Dear Hao Chen,

I think linux command “grep” and “tail" may helpful for you.

For example, if you have several job directories and each direcotires have standard output file named “job.out”,

You can get final energy of one job with following command

grep “total energy” jobdir/job.out|grep “^!”|tail -n 1

You can also use above command in for loop (bash script)

for i in jobdir1 jobdir2 jobdir3
do
grep “total energy” jobdir/job.out|grep “^!”|tail -n 1
done

for loop can also be used when you submit your multiple pw.x jobs

for celldim in `seq 10.0 0.1 10.4 `
do
mkdir cell_${celldim}
cat > cell_${celldim}/in.pw.x << EOF
&CONTROL
calculation ='scf',
verbosity = 'high',
restart_mode='from_scratch',
pseudo_dir='/home/mino/psp',
outdir='output',
tstress = .true.,
/
&SYSTEM
ibrav = 1,
celldm(1) = ${celldim},
nat = 8,
ntyp = 1,
ecutwfc = 35,
ecutrho = 280,
occupations = 'fixed',
smearing = 'gauss',
degauss = 0.02,
nosym=.true.,
noncolin=.true.,
lspinorb=.true.
nbnd =50,
/
&ELECTRONS
conv_thr = 1.D-6,
mixing_beta = 0.3,
/
&IONS
ion_dynamics = 'bfgs',
/
&CELL
cell_dynamics = 'bfgs',
cell_dofree = 'volume',
/
ATOMIC_SPECIES
Si 28.0855 Si.UPF
ATOMIC_POSITIONS (crystal)
Si 0.00000 0.00000 0.00000
Si 0.00000 0.50000 0.50000
Si 0.50000 0.50000 0.00000
Si 0.50000 0.00000 0.50000
Si 0.75000 0.25000 0.75000
Si 0.25000 0.25000 0.25000
Si 0.25000 0.75000 0.75000
Si 0.75000 0.75000 0.25000
K_POINTS automatic
1 1 1 0 0 0
EOF

cd cell_${celldim}
mpirun -np 28 /usr/local//src/qe-6.3/bin/pw.x < in.pw.x > job.dat
cd ..

done

Good Luck :)


Minho Lee

------------------------
Minho Lee
CEO/Developer
T. 02-3293-0204 | C. 010-2770-4080
E. mino at virtuallab.co.kr | H. http://www.virtuallab.co.kr

On-demand Materials Simulation
https://www.materialssquare.com
On 28 Aug 2018, 10:38 AM +0900, Hao Chen <chenhao.hitgucas at gmail.com>, wrote:
> Dear Dr. Stephen Weitzner
>
> Thanks very much. Would you like to let me know which example I should look at? Thanks again.
>
> Cheers!
>
> Hao
>
> > Weitzner, Stephen Eric <weitzner1 at llnl.gov> 于2018年8月27日周一 下午8:22写道：
> > > Hi Hao,
> > >
> > > If you take a look at one of the PWscf examples, specifically one of the “run_example” shell scripts, you can find an example for how to do what you are asking. The book Stefano suggested will teach you how to write such scripts. There are also free alternatives online that are just a google search away.
> > >
> > > Good luck.
> > >
> > > --
> > > Stephen Weitzner, PhD
> > > Postdoctoral Research Scientist
> > > Quantum Simulations Group
> > > Lawrence Livermore National Laboratory
> > >
> > >
> > > From: users <users-bounces at lists.quantum-espresso.org> on behalf of Hao Chen <chenhao.hitgucas at gmail.com>
> > > Reply-To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> > > Date: Monday, August 27, 2018 at 5:12 PM
> > > To: "users at lists.quantum-espresso.org" <users at lists.quantum-espresso.org>
> > > Subject: Re: [QE-users] How to carry out a series of simulations at the same time and output the stress and energy to one file?
> > >
> > > Thanks. I mean is there some command like in LAMMPS that can carry out simulations multitimes with just changing the parameters and output to the same file?
> > >
> > > Stefano Baroni <baroni at sissa.it> 于2018年8月27日周一 下午7:08写道：
> > > > https://www.dummies.com/DummiesTitle/UNIX-For-Dummies-5th-Edition.productCd-0764541471.html
> > > > ___
> > > > Stefano Baroni, Trieste -- http://stefano.baroni.me
> > > >
> > > > On 28 Aug 2018, at 02:01, Hao Chen <chenhao.hitgucas at gmail.com> wrote:
> > > > > Dear All
> > > > >
> > > > >      I am a beginner of quantum espresso. I tried to run single simulations and it seem to work now. What I want to investigate is the phase transformation process of silicon. I need carry out a bunch of simulations with different lattice constants. I want to output the energy and the stress state to one file. Do anyone know which command I should use for this purpose? Thanks very much!
> > > > >
> > > > > Wish you all the best!
> > > > >
> > > > > Hao
> > > > > _______________________________________________
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