[ase-users] ase-users Digest, Vol 115, Issue 4
Abid Channa
abid_channa04 at yahoo.com
Sat Jan 6 12:25:57 CET 2018
Hey Jens Jorgen,
Thanks for the script . Your effort is highly appreciated.
Best,
___________________________________
ABID ALI
PhD (Marie Curie-ITN) FellowTheoretical ChemistryScience Institute, University of Iceland
Dunhagi 3, VR-IIl
107 Reykjavik, IcelandMobile : 003547835935
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Subject: ase-users Digest, Vol 115, Issue 4
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Today's Topics:
1. Re: hcp0001 surface of La2O3 (Ask Hjorth Larsen)
2. Structure Optimization in NEB via Vasp (Dennis Trujillo)
3. Structure Optimization in NEB via Vasp (Dennis Trujillo)
4. Re: EMT-PES Script (Jens J?rgen Mortensen)
----------------------------------------------------------------------
Message: 1
Date: Thu, 4 Jan 2018 17:21:03 +0100
From: Ask Hjorth Larsen <asklarsen at gmail.com>
To: Punit Kumar <ip.punit.2016 at gmail.com>
Cc: ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] hcp0001 surface of La2O3
Message-ID:
<CACu53wn1Bhknuhn6A6yb6RaJDoRDHY44uOVqe5Rbd=UkePLS0w at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi Punit,
2018-01-01 6:56 GMT+01:00 Punit Kumar via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Hello ase-users and a very Happy New Year
>
> I would like to follow up making sure that the ase users got my previous
> mail. Any help is highly appreciated.
>
> Thank You
> Punit
> IIT Bombay
>
> On 25 December 2017 at 12:14, Punit Kumar <ip.punit.2016 at gmail.com> wrote:
>>
>> Hello ase-users
>>
>> I want to make an hcp0001 surface for La and La2O3 from their bulk crystal
>> structure. I have made bulk crystal structure of La and La2O3 using
>> 'crystal' function from 'spacegroup' module.
>>
>> >>> la = crystal(['La','La'], [(0., 0., 0.), (1./3.,2./3.,1./4.)],
>> >>> spacegroup=194, cellpar=[3.77, 3.77, 12.06, 90, 90, 120])
>>
>> >>> la2o3 = crystal(['La','O'], [(1./3., 2./3., 1./4.), (1./4., 1./4.,
>> >>> 0.)], spacegroup=150, cellpar=[3.93, 3.93, 6.13, 90, 90, 120])
>>
>> now after making the bulk crystal structure, I tried to make make hcp0001
>> surface for La and La2O3 using 'surface' function from build module.
>>
>> >>> la0001_1 = surface('la', (1,1,1), 3, vacuum=10)
This will not work because of lower-case l.
Can you provide a single script which runs?
>>
>> But when I compare this surface with the surface
>>
>> >>>la0001_2 = hcp0001('La', size=(2,2,3), a = 3.77, c = 12.06, vacuum =
>> >>> 10)
c should not be around 6?
>>
>> these two surfaces are very different from each other. In la0001_2 surface
>> one can see the layers very clearly while in la0001_1 surface layers are not
>> visible as in la0001_2 surface. All atoms in the layer of la0001_1 are
>> showing tag = 0.
But should they be equal? No surface type was specified when creating la0001_1.
Best regards
Ask
>> The same thing i have done for La2O3. What all I want is to make an
>> hcp0001 surface for La2O3 from its bulk crystal structure.
>> Can anyone help me in this matter. Any help is highly appreciated.
>>
>> With Best Regards
>> Punit
>> IIT Bombay
>
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
------------------------------
Message: 2
Date: Thu, 4 Jan 2018 14:11:35 -0500
From: Dennis Trujillo <dptru10 at gmail.com>
To: Eric Hermes via ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: [ase-users] Structure Optimization in NEB via Vasp
Message-ID: <FBEB5466-E8C9-4DCA-B9AC-5D73FFC820B9 at gmail.com>
Content-Type: text/plain; charset="us-ascii"
Hello *,
I am running a NEB calculation via the Vasp calculator, utilizing the BFGS optimizer. The initial structure is not converging and no information is being written to the trajectory file after ~700 ionic steps. The initial structure used was relaxed using Vasp manually outside of ASE. Any ideas as to how to make this structure converge faster? Attached is my script.
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Thanks
-Dennis
------------------------------
Message: 3
Date: Thu, 4 Jan 2018 14:10:24 -0500
From: Dennis Trujillo <dennis.trujillo at uconn.edu>
To: Eric Hermes via ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: [ase-users] Structure Optimization in NEB via Vasp
Message-ID: <929D642F-30D2-4094-A88B-3C00A1531E1E at uconn.edu>
Content-Type: text/plain; charset="us-ascii"
Hello *,
I am running a NEB calculation via the Vasp calculator, utilizing the BFGS optimizer. The initial structure is not converging and no information is being written to the trajectory file after ~700 ionic steps. The initial structure used was relaxed using Vasp manually outside of ASE. Any ideas as to how to make this structure converge faster? Attached is my script.
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Thanks
-Dennis
------------------------------
Message: 4
Date: Thu, 4 Jan 2018 20:32:38 +0100
From: Jens J?rgen Mortensen <jjmo at dtu.dk>
To: Abid Channa <abid_channa04 at yahoo.com>, ase-users
<ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] EMT-PES Script
Message-ID: <1336a13b-e31f-0b98-70f5-8d99bce96ea2 at dtu.dk>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Den 04-01-2018 kl. 15:28 skrev Abid Channa:
> Hey,
>
> Thanks for your reply. Basically my problem is
>
> *" Construct a Potential energy surface (PES) of the Pt(111) probing
> the surface with Pt atom, i.e. scan the surface with a Pt atom in
> which x and y coordinates are fixed and only the z coordinate is
> allowed to relax using EMT potential".*
>
> So, I am finding a script (How to generate array of positions and loop
> over array, for suppose I am selecting 10 points on surface) for
> generating a PES of my desired system like fcc, Pt111.
>
> I am very beginner in this field just started my work here.
I've attached a script showing one way to do it that you can play with.
(Please send to the list; re-added list to recipients)
Jens J?rgen
>
> Best,
>
> /___________________________________
> /
> ABID? ALI
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Jens J?rgen Mortensen <jjmo at dtu.dk>
> *To:* Abid Channa <abid_channa04 at yahoo.com>;
> "ase-users at listserv.fysik.dtu.dk" <ase-users at listserv.fysik.dtu.dk>
> *Sent:* Tuesday, January 2, 2018 1:26 PM
> *Subject:* Re: [ase-users] EMT-PES Script
>
> On 12/25/2017 12:11 PM, Abid Channa via ase-users wrote:
> > Hello ASE users,
> >
> > I am new in this field , I have just followed the tutorials available
> > at ASE site. Now I want to construct Potential Energy Surface of
> > ?Pt111 as Pt adatom using EMT.
> >
> > I have already overviewed several research papers related this. But I
> > am searching suitable script for constructing this PES. Any idea about
> > this, suggestions are requested.
>
> Can you be more specific about what kind of PES it is you would like to
> calculate?
>
> Jens J?rgen
>
>
> >
> > Best Regards,
> >
> > /___________________________________
> > /
> > ABID? ALI
> >
> > PhD (Marie Curie-ITN) Fellow
> > Theoretical Chemistry
> > Science Institute, University of Iceland
> > Dunhagi 3, VR-IIl
> > 107 Reykjavik, Iceland
> > Mobile : 003547835935
>
> >
> >
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk <mailto:ase-users at listserv.fysik.dtu.dk>
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
>
>
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