[ase-users] [EXTERNAL] Re: Espresso output files vibrational analysis

Wed Aug 14 18:48:48 CEST 2019

Dear Eric and ASE friends,

I’m very grateful to your response and explanation.

I have changed my script as you suggested and I’m currently testing.
I can already report that it looks quite promising, since I don’t have the error message as before.

Might it be an idea to give a warning when the vib object is created and no calculator is set on the atoms object?
At least the user has a hint where to search.

Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,

Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 14 Aug 2019, at 17:24, Hermes, Eric <ehermes at sandia.gov<mailto:ehermes at sandia.gov>> wrote:

Willem,

It would appear that the Vibrations class tries to determine the calculator attached to your atoms object when “vib” is initialized. In your script, this “slab” has no calculator object until after “vib” is created. You can solve this problem by putting the line “vib = Vibrations(…)” into the “with SocketIOCalculator(…) as calc:” block, after “slab.calc = calc”. We should probably also change Vibrations to behave more like Dynamics in this regard.

--
Eric Hermes
Postdoctoral Researcher
Sandia National Laboratories

From: <ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk>> on behalf of Offermans Willem via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Reply-To: Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be>>
Date: Wednesday, August 14, 2019 at 03:50
To: Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>>
Cc: ase users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: [EXTERNAL] Re: [ase-users] Espresso output files vibrational analysis

Dear Ask and ASE friends,

I have tried to run the vibration calculations with the socket interface.

I have changed a couple of things in my script:

<snip>

...

#    execQE = '/data/users/Public/woffermans/q-e/bin/pw-6.4.1.x < PREFIX.pwi > PREFIX.pwo'
    unixsocket = 'ase_espresso_Pd221_OHbridge17_5M3V2x1'
    execQE = ('/data/users/Public/woffermans/q-e/bin/pw-6.4.1.x < PREFIX.pwi --ipi {unixsocket}:UNIX > PREFIX.pwo'
           .format(unixsocket=unixsocket))
…

#    slab.set_calculator(espresso)

    vib = Vibrations(slab,indices=(0,1,2,3,4,5,6,7,38,40))

    dyn = BFGS(slab,trajectory=TrajectoryFile,restart='Pd221_OHbridge17_5M3V2x1.pckl',logfile='Pd221_OHbridge17_5M3V2x1.log')

    try:
        with SocketIOCalculator(espresso, log=sys.stdout,
                        unixsocket=unixsocket) as calc:
            slab.calc = calc
#            dyn.run(fmax=0.02)
            vib.run()

…

</snip>

Although the script works for relaxation (dyn.run(fmax=0.02)), it doesn’t work for vibrations.

I got the following error message:

ase.calculators.calculator.PropertyNotImplementedError: The property "forces" is not available.

Has someone run a vibration calculation with the socket interface?
If yes, could you share (the important part of) the code?

Can someone point out what I did wrong?

Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,

Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.bethe<mailto:Willem.Offermans at Vito.bethe>

<image001.jpg>

On 19 Jul 2019, at 16:47, Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>> wrote:

Dear Willem,

Am Fr., 19. Juli 2019 um 15:45 Uhr schrieb Offermans Willem via
ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:

Dear ASE friends,

When I run vibrational calculation with ASE and Quantum Espresso, intermediate output files of QE are dismissed.
However, I would like to save and have a view into these intermediate files.
Is this possible? Maybe by some code hacking? Where is the best place to hack this into the code?

Answer 1: Use the socket interface, which will also make the
calculation run faster.
https://wiki.fysik.dtu.dk/ase/dev/ase/calculators/socketio/socketio.html

Answer 2:  Optimizers now have an irun() method which allows for _ in
opt.irun(): <any code>  We'd like to provide an irun() method for
Vibrations as well.  This would allow the user to set the calculator
directory for each calculation, also for those calculators that don't
support the socket interface.  There's also a merge request for
automatically updating the calculation directory of a calculator for
each calculation triggered, but this is on hold.  Either way, answer 1
is the Good solution.

Best regards
Ask

Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,

Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

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