Re: [SIESTA-L] constrain moves

[Nick Papior]

On 16 Apr 2016 20:57, "Mostafa Shabani" 
wrote:
>
> Dear siesta users
>
> For 20 atoms in unit cell we want to constrain all atoms moves in all
directions except for atoms number 11 and 16 that are fixes just in x and y
directions and are free to move in z direction.
>
> W use this block GeometryConstraints in fdf input file
>
>
> %block GeometryConstraints
>
> position from -1 to -10
> position from -12 to -15
> position from -17 to -20
> center 11 16 1.0  0.0  0.0
> center 11 16 0.0  1.0  0.0
>
> %endblock GeometryConstraints
>
> is it true?
No, why would you use negative indices?
You should be able to achieve your desired effect with this:
%block GeometryConstraints
position from 1 to 10
position from 12 to 15
position from 17 to 20
position 11 16 1.0  0.0  0.0
position 11 16 0.0  1.0  0.0
%endblock GeometryConstraints
>
>
> Thanks in advance
>

[SIESTA-L] constrain moves

[Mostafa Shabani]

Dear siesta users

For 20 atoms in unit cell we want to constrain all atoms moves in all
directions except for atoms number 11 and 16 that are fixes just in x and y
directions and are free to move in z direction.

W use this block GeometryConstraints in fdf input file


%block GeometryConstraints

position from -1 to -10
position from -12 to -15
position from -17 to -20
center 11 16 1.0  0.0  0.0
center 11 16 0.0  1.0  0.0

%endblock GeometryConstraints

is it true?


*Thanks in advance*

Re: [SIESTA-L] transiesta doesn't converge

[Raha khalili]

Dear Rajan and Transiesta users,

I changed the atomic coordination as you said but the scattering region
calculation didn't get converged and got aborted after ten days. Here are
attached my input files. First, I did electrode calculations in separate
directories and then copied Left/Right.TSHS file in scattering calculation
directory. Could you help me please to find the problem?

Thank you in advance,
Kind regards,
Raha

On Tue, Mar 29, 2016 at 9:33 PM, RAJAN SINGH 
wrote:

> Dear Raha
>
> I think atleast one atom of your left electrode's  z-coordinate has to be
> zero. other x and y coordinates may not be zero i think
>
> regards
> Rajan
>
> On Sun, Mar 27, 2016 at 11:29 AM, Nick Papior 
> wrote:
>
>> I haven't checked your right electrode, but your input coordinates for
>> the left electrode are very wrong...
>>
>> --
>>
>> Kind regards Nick Papior
>> On 26 Mar 2016 08:20, "Raha khalili"  wrote:
>>
>>> Dear Transiessta users,
>>>
>>> I am trying to find transmission of a molecular junction consisting of a
>>> single-molecule sandwiched between two gold contacts with Transiesta.
>>> Everything is Ok for left and right electrodes but the calculation for
>>> whole system get aborted by cluster system after around ten days foe
>>> several times. I don't know whether this is a problem related to my input
>>> files or not.
>>>
>>> Here are attached the input file for electrodes and scattering region.
>>> Any suggestion will be appreciated.
>>>
>>> Best wishes,
>>> Raha
>>>
>>> --
>>> Khadijeh Khalili
>>> Nanotechnology group, Physics department, university of Mazandaran
>>> Babolsar, Iran
>>>
>>
>


-- 
Khadijeh Khalili
Nanotechnology group, Physics department, university of Mazandaran
Babolsar, Iran


RUN-scat.fdf
Description: application/vnd.fdf


RUN-right.fdf
Description: application/vnd.fdf


RUN-left.fdf
Description: application/vnd.fdf