[DFTB-Plus-User] How to set the pressure at a certain direction?

Wed Sep 4 04:42:32 CEST 2019

Thanks for your kind reply.

Best regards,
Yecheng Shao

Zhejiang University

发件人: dftb-plus-user-request at mailman.zfn.uni-bremen.de
发送时间: 2019年9月3日 21:45
收件人: dftb-plus-user at mailman.zfn.uni-bremen.de
主题: DFTB-Plus-User Digest, Vol 61, Issue 1

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Today's Topics:

   1. Re: NPT simulation-md trj (Bálint Aradi)
   2. Re: How to set the pressure at a certain direction?
      (Bálint Aradi)
   3. Similar files give different results in DFTB-NGEF
      transportOnly calculations (Amit Gupta)

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Message: 1
Date: Tue, 3 Sep 2019 14:05:35 +0200
From: Bálint Aradi <aradi at uni-bremen.de>
To: dftb-plus-user at mailman.zfn.uni-bremen.de
Subject: Re: [DFTB-Plus-User] NPT simulation-md trj
Message-ID: <38677c4b-956a-9ba6-db47-72812ad2b8db at uni-bremen.de>
Content-Type: text/plain; charset="utf-8"

Dear Simin,

> II have 2 questions and any help is appreciated. 1) I want to know
> how to set input in order to write the trajectory of NPT md
> calculation down , I mean to have also box information inside the
> trajectory, for example pdb format.

Currently, we output the lattice vectors in the md.out file.

> 2) In non-scc-md run, some md steps is  written several times in xyz 
> output ( md iter  number is same for some written configurations in
> xyz output file) . why? Are these belong to non converged
> calculations or something like this?

That's interesting, that should not be the case. I just tried a non-scc
MD run, but can't reproduce your error. Is it possible, that you send me
off-list a reproducable example, where it occurs?

  Best regards,

  Bálint

-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/

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Message: 2
Date: Tue, 3 Sep 2019 14:16:41 +0200
From: Bálint Aradi <aradi at uni-bremen.de>
To: dftb-plus-user at mailman.zfn.uni-bremen.de
Subject: Re: [DFTB-Plus-User] How to set the pressure at a certain
	direction?
Message-ID: <635ccc3b-92b2-fb64-ab1b-c2a2c1b92ee6 at uni-bremen.de>
Content-Type: text/plain; charset="utf-8"

Dear Yecheng,

> However, the pressure in Driver only support one dimension value,
> how can I optimized the structure when I try to stretch in one
> dimension while keeping the pressure on rest directions at specified
> nonzero value, eg., stretching 20% strain in x direction while keep
> the pressure on y as 100GPa and z as 200GPa.

Currently, you can only specify the isotropic pressure in the
simulations. Although internally, we work with the full stress tensor,
the user interface currently only allows a scalar value.

> Ps. How is the pressure of simulation box related to the stress
> tensor?

The diagonal components of the stress tensor would be set to the
external pressure values provided by the user, see

https://github.com/dftbplus/dftbplus/blob/ed9ff63f15fa74fe899c8d4e77d73f44299b2b1f/prog/dftb%2B/lib_md/velocityverlet.F90#L208

  Best regards,

  Bálint

-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/

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Message: 3
Date: Tue, 3 Sep 2019 19:14:26 +0530
From: Amit Gupta <amitg at tifrh.res.in>
To: dftb-plus-user at mailman.zfn.uni-bremen.de
Subject: [DFTB-Plus-User] Similar files give different results in
	DFTB-NGEF	transportOnly calculations
Message-ID:
	<CAMO8CMa41YSUzQ1TdFH2t5=5zdX4rtNY+yfR00OE9J0pi_pMmQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I picked the device_7.gen file from the examples and removed its hydrogens
for an experiment I am running. It works fine and I am able to get the
transmissions graph.
But when I created my own file from vmd, with almost exact same structure,
I get almost zero transmission. Its quite perplexing to be honest. What am
I doing wrong?

I am attaching a tar file with a minimum working example. to run any file,
just comment out the 2-3 line in dftb_in.hsd file. Everything else remains
the same.

Thank you
Attachment content:
device_7.gen file: dehydrogenated graphene ribbon from the provided DFTB+
example tutorial
pristine_2_aligned.gen file: my own graphene ribbon of same dimensions and
structure
*.xyz: xyz files of above *.gen files
C-C.skf: SK file for graphene
dftb_in.hsd: dftb input file for running the example
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