[DFTB-Plus-User] NEMD MD with DFTB+

Goldman, Nir goldman14 at llnl.gov
Wed Jun 22 22:00:04 CEST 2022 

Dear Ankur,

Thanks for your note and interest in LAMMPS/DFTB+. You can indeed use LATTE with LAMMPS. Historically LATTE uses quite a bit different methodology than DFTB+, and so the results from each could vary.

Best,

Nir

--
Nir Goldman
Material Sciences Division, PLS
Lawrence Livermore National Laboratory
P.O. Box 808, L-285
Livermore, CA 94551-0808
Phone: (925) 422-3994
https://people.llnl.gov/goldman14

From: Ankur Gupta <ankur at lbl.gov>
Date: Wednesday, June 22, 2022 at 11:52 AM
To: User list for DFTB+ related questions <dftb-plus-user at mailman.zfn.uni-bremen.de>
Cc: "Goldman, Nir" <goldman14 at llnl.gov>
Subject: Re: [DFTB-Plus-User] NEMD MD with DFTB+

Dear Dr. Goldman,

I am also quite interested in using Lammps functionalities with DFTB+ methods. I am especially interested in using GFN2-xTB methods through Lammps. Also, it seems like one can install the LATTE package in Lammps to use the DFTB methods; however, it probably doesn't have all the Hamiltonians of DFTB+.

Best,
Ankur

On Wed, Jun 22, 2022 at 11:13 AM Goldman, Nir via DFTB-Plus-User <dftb-plus-user at mailman.zfn.uni-bremen.de<mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>> wrote:
Dear Ali,

It's possible that you can get some of the MD functionality you mention through LAMMPS, if you haven't explored it already. We're currently working on a LAMMPS/DFTB+ interface that you might be able to use in the near future. Please feel free to reach out later in the summer to check on the status of all of that.

Best,

Nir

--
Nir Goldman
Material Sciences Division, PLS
Lawrence Livermore National Laboratory
P.O. Box 808, L-285
Livermore, CA 94551-0808
Phone: (925) 422-3994
https://people.llnl.gov/goldman14

On 6/21/22, 5:39 AM, "DFTB-Plus-User on behalf of Bálint Aradi" <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de<mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> on behalf of aradi at uni-bremen.de<mailto:aradi at uni-bremen.de>> wrote:

    Dear Ali,

    indeed, you can only apply isotropic pressure in DFTB+. And yes, the
    non-equilibrium transport (via Greens functions) refers to the
    electronic system (e.g. when you apply bias to your systems via
    contacts), so this is not what you are looking for.

    Unfortunately, I am definitely not an MD expert, so I am not sure, what
    would be the right way to simulate you system.

    Best regards,

    Bálint

    On 17.06.22 17:53, Alathea Davies wrote:
    > Hello!
    >
    > I am hoping to conduct desalination simulations utilizing the MD
    > functionality of DFTB+. I've been able to look at self diffusion between
    > water, NaCl, and my membranes, and what I would like to do next is to
    > apply a pressure difference in my simulation cell to simulate
    > desalination. This would require setting the pressure at one end of my
    > simulation cell different from the pressure at the other end. My
    > intention is to apply pressure in the z-direction and periodic boundary
    > conditions in both x- and y-. However, it doesn't seem that I would be
    > able to do this with DFTB+. My understanding is that I can only define
    > one external pressure around my entire periodic system, rather than
    > defining different pressures at different boundaries. I've been reading
    > through the manual extensively and searching online, but I can't come to
    > a conclusive answer whether I'd be able to perform these simulations or
    > if there is a work-around to do this with DFTB+. My two questions, then,
    > are:
    >
    >  1. Does DFTB+ do non-equilibrium MD? Would other users have suggestions
    >     how I could perform these calculations with DFTB+?
    >
    >  2. I understand that DFTB+ has the "Transport" calculations, but from
    >     my understanding in the manual, these are more quantum mechanics
    >     based transport (electrons, phonons, etc.) then mass transport. Am I
    >     understanding this correctly?
    >
    > If there are any suggestions regarding how I could use DFTB+ MD
    > functionality to conduct pressure-driven desalination simulations, I
    > would be very grateful to hear them!
    >
    > Thank you so much for your help!
    >
    > ~ Alathea (Ali) Davies
    >
    >
    > Graduate Research Assistant
    > Computational Design Research Group
    > University of Wyoming
    > Department of Chemistry
    > adavies2 at uwyo.edu<mailto:adavies2 at uwyo.edu>
    >
    >
    > _______________________________________________
    > DFTB-Plus-User mailing list
    > DFTB-Plus-User at mailman.zfn.uni-bremen.de<mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
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    --
    Dr. Bálint Aradi
    Bremen Center for Computational Materials Science, University of Bremen
    http://www.bccms.uni-bremen.de/cms/people/b-aradi/<https://urldefense.us/v3/__http:/www.bccms.uni-bremen.de/cms/people/b-aradi/__;!!G2kpM7uM-TzIFchu!lp3KB6qjcuET2oyhPTPJ3_9w3C-ZplD1MbLHMVRRiBMQhYSBMFPy4ak_JafeEBJzHTc$>


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