[ase-users] Dimer

[Alaithan, Zainab]

Thanks a lot mike. it seems that I am blocked from downloading this file.  If you don't mind can you try sending it with a text extension. Perhaps I can download it.

Regards,
________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Michael Joseph Waters via ase-users <ase-users at listserv.fysik.dtu.dk>
Sent: 23 January 2020 16:16
To: Offermans Willem via ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] Dimer


This email from ase-users at listserv.fysik.dtu.dk originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.



I agree,

The MinModeAtoms/DimerAtoms objects are not well explained. The things I think are missing is setting/getting the dimer location and direction/eigenmode. I've been building my personal example on finding reaction pathways which shows how to do these things. It takes about 20 - 30 seconds to run. Feel free to use it and acknowledge me when you cure cancer!

Cheers,
-Mike


________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Offermans Willem via ase-users <ase-users at listserv.fysik.dtu.dk>
Sent: Thursday, January 23, 2020 8:49 AM
To: ase users <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] Dimer

Dear Zainab and ASE friends,

To my opinion, Zainab is missing basic documentation on how to use the dimer method with ASE.

How to restart a dimer calculation?
How to monitor convergence?
How to identify the possible transitions state in the trajectory file?
How to retrieve the energy of the possible transition state?
How to retrieve the remaining forces of the possible transition state?



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 23 Jan 2020, at 15:29, Michael Joseph Waters via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Hi Zainab,

You may want to try changing your optimizer. The documentation lists: BFGS, BFGSLineSearch, LBFGS, LBFGSLineSearch, GPMin, MDMin and FIRE as options. Many of the optimizers have options for maxstep/maxmove which limit large position jumps. Some optimizers have a damping option which can help.


Are you using molecular mechanics or an ab initio method like DFT for your dimer calculations?

If you are using molecular mechanics, try extending your cut-off distances.

If you are using an ab initio method, increasing your spatial sampling/plane wave cutoff and using tighter energy tolerances can help. If you are working with a spin-polarized ab initio method, things can get trickier due to the coexistence of multiple spin PES.

Best,
-Mike
________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk> <ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk>> on behalf of Alaithan, Zainab via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Sent: Thursday, January 23, 2020 7:06 AM
To: Ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: [ase-users] Dimer

Dear Ase-user,

Can someone please share some tips about how to restart the dimer calculation from the dimer trajectory? and what is the appropriate displacement vector in this case? especially if the dimer calculation was converging and I just want to tighten the convergence criteria.

I will appreciate any help.

Regards,
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