[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 69, Issue 3

Mon Oct 14 13:40:46 CEST 2013

---------------------------- Original Message ----------------------------
Subject: Re: DFTB-Plus-User Digest, Vol 69, Issue 3
From:    n.salami at srbiau.ac.ir
Date:    Mon, October 14, 2013 10:22 am
To:      dftb-plus-user at dftb-plus.info
--------------------------------------------------------------------------

Dear Gabrielle,
Good time.

thank you for your swift response.
for building SiNW in different direction, I want install Nanocut program,
for this I have installed Python3.3 as follow:

tar zxvf Python-3.3.2.tar.xz
./configure --prefix=/opt/python3.3
make
make test
make altinstall

 after that I have downloaded NumPy version 1.7.1, then I have unzipped
it, and I have installed it by interring these commands in the terminal:
cd numpy
sudo python3 setup.py install

Finally, I have unzipped Nanocut program and I have installed it by
interring these commands in the terminal:
 cd nanocut
 sudo python3 setup.py install --prefix ~/opt/nanocut

but

when I have entered this conmmand in terminal for checking installation of
Nanocut:
~/opt/nanocut/bin/nanocut -h

, I faced to this error

"Traceback (most recent call last):
  File "/home/salami/opt/nanocut/bin/nanocut", line 3, in <module>
    import numpy as np
ImportError: No module named numpy"

Could you help me to solve this problem, please?

Tanks in advance.
Best Regards,
Nadia Salami,

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> Today's Topics:
>
>    1. transitional vectors for SiNW (n.salami at srbiau.ac.ir)
>    2. Re: transitional vectors for SiNW (Riccardo Petraglia)
>    3. Re: transitional vectors for SiNW (Gabriele Penazzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 Oct 2013 10:07:43 -0000
> From: n.salami at srbiau.ac.ir
> To: dftb-plus-user at dftb-plus.info
> Subject: [DFTB-Plus-User] transitional vectors for SiNW
> Message-ID:
> 	<43f9794813ed09ad035a429b3a09f84e.squirrel at mail.srbiau.ac.ir>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear users,
>
> I'm trying to build silicon nanowire in big diameter for example 5nm
> diameter in 110 direction for calculation of transport properties.for
> this, I used geometry of SiNW in 1.2nm diameter from examples of
> DFTB+NEQF, then I deleted Hydrogen atoms, after that I must replicated the
> supercell, but I don't know the transitional vectors in this direction.
> I installed python2.7 and dptools, but I don't know correct command of
> running xyz2gen for getting the lattice vectors.
> As I'm beginner of DFTB+NEGF, So please help me to solve my problem.
>
> Tanks in advance.
> Nadia Salami
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 07 Oct 2013 17:11:58 +0200
> From: Riccardo Petraglia <riccardo.petraglia at epfl.ch>
> To: User list for DFTB+ related questions
> 	<dftb-plus-user at dftb-plus.info>
> Subject: Re: [DFTB-Plus-User] transitional vectors for SiNW
> Message-ID: <5252CF3E.60505 at epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
> I generated the gen file from the xyz and than I added the lattice
> vectors in the gen file as described at page 51 of the manual (appendix
> C).
>
> You are welcome ;)
> Riccardo Petraglia
>
> On 10/07/2013 12:07 PM, n.salami at srbiau.ac.ir wrote:
>> Dear users,
>>
>> I'm trying to build silicon nanowire in big diameter for example 5nm
>> diameter in 110 direction for calculation of transport properties.for
>> this, I used geometry of SiNW in 1.2nm diameter from examples of
>> DFTB+NEQF, then I deleted Hydrogen atoms, after that I must replicated
>> the
>> supercell, but I don't know the transitional vectors in this direction.
>> I installed python2.7 and dptools, but I don't know correct command of
>> running xyz2gen for getting the lattice vectors.
>> As I'm beginner of DFTB+NEGF, So please help me to solve my problem.
>>
>> Tanks in advance.
>> Nadia Salami
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 07 Oct 2013 17:53:37 +0200
> From: Gabriele Penazzi <gabriele.penazzi at bccms.uni-bremen.de>
> To: dftb-plus-user at dftb-plus.info
> Subject: Re: [DFTB-Plus-User] transitional vectors for SiNW
> Message-ID: <5252D901.2090109 at bccms.uni-bremen.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 10/07/2013 12:07 PM, n.salami at srbiau.ac.ir wrote:
>> Dear users,
>>
>> I'm trying to build silicon nanowire in big diameter for example 5nm
>> diameter in 110 direction for calculation of transport properties.for
>> this, I used geometry of SiNW in 1.2nm diameter from examples of
>> DFTB+NEQF, then I deleted Hydrogen atoms, after that I must replicated
>> the
>> supercell, but I don't know the transitional vectors in this direction.
>
> Hi,
>
> be aware that the structure in the example has been relaxed and not just
> built by repeting the bulk unit cells, therefore what you won't get what
> you expect.
>
> You'll have to build the structure yourself by starting from bulk
> silicon, you can help yourself using some ready to go tools, for example:
>
> ASE: https://wiki.fysik.dtu.dk/ase/?
> Nanocut: https://bitbucket.org/aradi/nanocut
> Avogadro: http://avogadro.openmolecules.net/wiki/Main_Page
>
> and probably many others
> Also, a 5nm diameter is a lot, you could want to rethink your
> expectations.
>
> Best,
> Gabriele
>
>
>> I installed python2.7 and dptools, but I don't know correct command of
>> running xyz2gen for getting the lattice vectors.
>> As I'm beginner of DFTB+NEGF, So please help me to solve my problem.
>>
>> Tanks in advance.
>> Nadia Salami
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
> --
> Dr. Gabriele Penazzi
> BCCMS - University of Bremen
>
> http://www.bccms.uni-bremen.de/
> http://sites.google.com/site/gabrielepenazzi/
>
> phone: +49 (0) 421 218 62337
> fax: +49 (0) 421 218 62770
>
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> End of DFTB-Plus-User Digest, Vol 69, Issue 3
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