[DFTB-Plus-User] How to generate s-k files?

[李捷]

Thank you very much for your reply. BTW, there was one email before that
regarding the question of generating the s-k files. I am not sure if you
have seen it.  I appreciate it a lot if you can give me some suggestions on
this. Below is a copy of that email.

"Dear Dr. Aradi
Thank you very much for sending me the files and I appreciate it a lot for
your help. I will try to do some calculations of the system I am studying
using the the files you sent me and see what will the result looks like.

BTW, correct me if I am wrong, my understanding is that the s-k files for
any element are highly dependable on the environment the element resides
in. For example, the s-k files for Cu and C should be different in an
environment where there are only Cu and C atoms (in case such a system
exists) to those in an environment where there are  Cu, C, H, and O in the
system.

If the statement above is true, the system I am studying indeed contains
Cu, C, H and O and the s-k files I don't have is between Cu and C. To
generate s-k files for Cu and C which can best fit my system, I was
wondering to start with some simple compound like CuHCO3 which includes all
the elements I need but are much simpler in structure and use Material
Studio to generate the s-k files. Please let me know if this is the right
approach to proceed or if there is anything I am doing wrong?

Thanks again for your help.

Best,

Jie"

On Fri, May 22, 2015 at 12:15 AM, MF <foster362 at gmail.com> wrote:

> Hi Jie,
>
> The regular version, DFTB+ 1.2, can use all the CPUs within a node
> (openMP). You need to set the environment variable OMP_NUM_THREADS to the
> number of threads/cores you want to use in your run script. You should be
> able to find ample information online about this. The mpi version is for
> running on multiple nodes and is only really useful for very large systems
> and computer systems with fast network connections (i.e. Infiniban)
>
> Cheers
>
> Sent from my iPhone
>
> On May 21, 2015, at 8:37 PM, 李捷 <lijielile at gmail.com> wrote:
>
> Dear Dr Aradi,
>
> The other question I have is regarding the version of DFTB I use. The DFTB+
> 1.2 version I believe is the standard version but it is not a parallel
> version (Correct me if I am wrong). I guess with this version I can't use
> all the cores of my computer's processors in parallel which could
> potentially compromise the calculation speed. Is it true that I have do
> download the DFTB+MPI or the DFTB+MPI-NEGF version for parallel computing
> and get the maximum out of all the cores?
>
> Thanks for your help.
>
> Best,
>
> Jie
>
> On Thu, May 21, 2015 at 8:46 PM, 李捷 <lijielile at gmail.com> wrote:
>
>> Dear Dr. Aradi
>> Thank you very much for sending me the files and I appreciate it a lot
>> for your help. I will try to do some calculations of the system I am
>> studying using the the files you sent me and see what will the result looks
>> like.
>>
>> BTW, correct me if I am wrong, my understanding is that the s-k files for
>> any element are highly dependable on the environment the element resides
>> in. For example, the s-k files for Cu and C should be different in an
>> environment where there are only Cu and C atoms (in case such a system
>> exists) to those in an environment where there are  Cu, C, H, and O in the
>> system.
>>
>> If the statement above is true, the system I am studying indeed contains
>> Cu, C, H and O and the s-k files I don't have is between Cu and C. To
>> generate s-k files for Cu and C which can best fit my system, I was
>> wondering to start with some simple compound like CuHCO3 which includes all
>> the elements I need but are much simpler in structure and use Material
>> Studio to generate the s-k files. Please let me know if this is the right
>> approach to proceed or if there is anything I am doing wrong?
>>
>> Thanks again for your help.
>>
>> Best,
>>
>> Jie
>>
>>
>> On Wed, May 20, 2015 at 7:17 AM, Bálint Aradi <aradi at uni-bremen.de>
>> wrote:
>>
>>> Dear Jie,
>>>
>>> > Thank you very much for your reply and information. I definitely would
>>> > like to try those files you mentioned but I can't find them from the
>>> > link you sent. I appreciate it a lot if you can let me know how can I
>>> > get them? We will definitely acknowledge your contribution in any
>>> > resulting publications.
>>>
>>> attached you find the Cu-C files we have used in the mentioned article.
>>>
>>>   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/
>>>
>>>
>>> _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>>
>>>
>>
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