[ase-users] ase-users Digest, Vol 140, Issue 8
Oscar Xavier Guerrero
oscarxavier.ox at gmail.com
Tue Feb 18 22:06:58 CET 2020
You're right. That was it. I guess I'll have to change my editor to catch
this kind of error.
Thank you very much.
Le mar. 18 févr. 2020 à 13:50, Maxime Van den Bossche via ase-users <
ase-users at listserv.fysik.dtu.dk> a écrit :
> Hi Oscar,
>
> With the runscript you provided, I could reproduce the behaviour you got
> and I was also a bit puzzled at first. Then I noticed a subtle typo: it
> should
> be "ps*e*udopotentials=..." (with e) instead of "psudopotentials=...".
>
> The incorrect spelling led the ASE calculator to use the default
> pseudopotentials
> dictionary, i.e. an empty one, and which then leads to *_dummy.UPF.
>
> The spelling is correct on the webpage, so something must have gone
> wrong when copying it.
>
> best,
> Maxime
>
>
> Op di 18 feb. 2020 om 11:08 schreef <
> ase-users-request at listserv.fysik.dtu.dk>:
>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 18 Feb 2020 10:06:08 -0600
>> From: Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>
>> To: ase-users <ase-users at listserv.fysik.dtu.dk>
>> Subject: Re: [ase-users] ase espresso example fail
>> Message-ID:
>> <CAM0Hkbe_KViTNhG+BQgJQP_HSv_ZqfwVmX=
>> XqdzuPkeztGaVHg at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Maxime,
>>
>> Thank you for your reply, here bellow I paste the requested information
>> and
>> a little extra in case you need it. In the meantime as a workaround and a
>> test, I copied the PPs to have the dummy names generated in by the script
>> and it ran fine.
>>
>> $ ase --version
>> ase-3.19.0
>>
>> The script I ran (I commented out the pseudo_dir parameter as it had the
>> same result):
>>
>> #!/usr/bin/env python3.8
>> *from* ase.build *import* bulk
>> * from* ase.calculators.espresso *import *Espresso
>> *from* ase.constraints *import *UnitCellFilter
>> *from *ase.optimize *import *LBFGS
>>
>> pseudopotentials = {'Na': 'Na.pbe-spn-rrkjus_psl.1.0.0.UPF',
>> 'Cl': 'Cl.pbe-nl-rrkjus_psl.1.0.0.UPF'}
>>
>> rocksalt = bulk('NaCl', crystalstructure='rocksalt', a=6.0)
>> calc = Espresso(psudopotentials=pseudopotentials,
>> #pseudo_dir='/home/oscar/quantum-espresso/pseudo/',
>> tstress=True, tprnfor=True, kpts=(3, 3, 3))
>> rocksalt.calc = calc
>> ucf = UnitCellFilter(rocksalt)
>> opt = LBFGS(ucf)
>> opt.run(fmax=0.005)
>> # cubic lattic constant
>> *print*((8*rocksalt.get_volume()/*len*(rocksalt))**(1.0/3.0))
>>
>> And here is the generated espresso.pwi file generated:
>>
>> &CONTROL
>> tstress = .true.
>> tprnfor = .true.
>> /
>> &SYSTEM
>> ntyp = 2
>> nat = 2
>> ibrav = 0
>> /
>> &ELECTRONS
>> /
>> &IONS
>> /
>> &CELL
>> /
>>
>> ATOMIC_SPECIES
>> Na 22.98976928 Na_dummy.UPF
>> Cl 35.45 Cl_dummy.UPF
>>
>> K_POINTS automatic
>> 3 3 3 0 0 0
>>
>> CELL_PARAMETERS angstrom
>> 0.00000000000000 2.82818982796933 2.82818982796933
>> 2.82818982796933 0.00000000000000 2.82818982796933
>> 2.82818982796933 2.82818982796933 0.00000000000000
>>
>> ATOMIC_POSITIONS angstrom
>> Na 0.0000000000 0.0000000000 0.0000000000
>> Cl 2.8281898280 0.0000000000 0.0000000000
>>
>>
>> Also, for the pseudopotentials:
>>
>> $ echo $ESPRESSO_PSEUDO
>> /home/oscar/quantum-espresso/pseudo/
>> $ ls /home/oscar/quantum-espresso/pseudo/{Na,Cl}*.UPF
>> /home/oscar/quantum-espresso/pseudo/Cl.pbe-nl-rrkjus_psl.1.0.0.UPF
>> /home/oscar/quantum-espresso/pseudo/Na.pbe-spn-rrkjus_psl.1.0.0.UPF
>>
>>
>>
>> Le mar. 18 f?vr. 2020 ? 03:07, Maxime Van den Bossche via ase-users <
>> ase-users at listserv.fysik.dtu.dk> a ?crit :
>>
>> > Dear Oscar,
>> >
>> > I did a quick check and the example runs fine on my end
>> > (wit the same adjustment of the 'pseudopotentials' dict).
>> > Could show you run script and ASE version?
>> >
>> > Best,
>> > Maxime
>>
>
>
>> >> Message: 2
>> >> Date: Mon, 17 Feb 2020 11:52:28 -0600
>> >> From: Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>
>> >> To: ase-users <ase-users at listserv.fysik.dtu.dk>
>> >> Subject: [ase-users] ase espresso example fail
>> >> Message-ID:
>> >> <
>> >> CAM0HkbcWLomHAehYSV+rYqObUaiGo9XVoFSL-RJKNJPFj9WQMQ at mail.gmail.com>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> Hi all,
>> >>
>> >> I'm trying to configure ase to run quantum-espresso. I followed the
>> setup
>> >> instructions <
>> https://wiki.fysik.dtu.dk/ase/ase/calculators/espresso.html>
>> >> and
>> >> ran the example calculation for NaCl but the calculation failed. The
>> >> espresso.in file has Na_dummy.UPF and Cl_dummy.UPF instead of the
>> >> pseudopotentials I provided in the dictionary. I even added the
>> pseudo_dir
>> >> optionto make sure it wasn't an error on the ESPRESSO_PSEUDO
>> environment
>> >> variable and got the same dummy PP file error. Running pw.x manually
>> from
>> >> the command line with the input file (modified to have the correct PP
>> >> names) works just fine.
>> >>
>> >> Why is ase writing dummy PP names and what can I do to fix this?
>> >>
>> >> Thank you in advance for your help
>> >>
>> >>
>> >> Oscar X. Guerrero Guti?rrez
>> >> Department of Chemistry
>> >> CINVESTAV
>> >>
>> > _______________________________________________
>> > ase-users mailing list
>> > ase-users at listserv.fysik.dtu.dk
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>>
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