[SIESTA-L] << Materials Modeling Stack Exchange >>

2020-06-17 Por tôpico I. Camps 
Dear SIESTers,

I would like to invite you to visit the Materials Modeling Stack Exchange
forum (in public beta).

The site is dedicated for those interested in building a community
dedicated to answering research level questions about molecular and
materials modeling.

https://materials.stackexchange.com/



[]'s,

Camps

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

2020-06-17 Por tôpico El-abed Haidar 
But also take into account Nick’s comment on contour and used atoms.
Also you might be careful on the cutoff energy maybe for your system 150 Ry 
could be enough.
But a convergence test would be more suitable first.
Good luck!

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder
Sent: Wednesday, 17 June 2020 6:15 AM
To: siesta-l@uam.es
Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Transport is along the z-direction, thanks for your help I will try to make use 
of those options.

‫في الاثنين، 15 يونيو 2020 في 11:02 م تمت كتابة ما يلي بواسطة ‪El-abed Haidar‏ 
<‪ehai2...@uni.sydney.edu.au‏>:
Hi Rayan
Quick question what is the transport direction?
I feel there are some essential blocks missing. Those are generally required 
for a TranSIESTA and TbTrans calculation. Good luck!

%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
  mu V/2
  contour.eq
begin
  c-Left
  t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
begin
  c-Right
  t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ./left.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
  used-atoms 63
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ./right.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
  used-atoms 63
%endblock TS.Elec.Right
TS.Contours.Eq.Pole2.5 eV
%block TS.Contour.c-Left
  part circle
   from -999.99893 eV + V/2 to -10. kT + V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from -999.99893 eV - V/2 to -10. kT - V/2
points 50
 method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
points 10
 method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta0.000100 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
 method mid-rule
%endblock TS.Contour.nEq.neq
# TBtrans options
TBT.T.Eig 5
TBT.Elecs.Eta0.136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from   -2.0 eV to2.0 eV
delta0.00800 eV
 method mid-rule
%endblock TBT.Contour.neq

TBT.DOS.A.All  true
TBT.CDF.MPI true
TS.Voltage 0.0 eV


El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006


From: rayan moukhadder
Sent: Monday, 15 June 2020 6:04 AM
To: siesta-l@uam.es
Subject: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Dear all,

I am a phd student and I am new to siesta , I am doing a Transiesta calculation 
for a system that consist of two graphene sheets sandwiching three cobalt 
atoms, as the electrode calculation is successfully done, the SCF iterations in 
SR calculation are not converging where my input file is

SystemName  SR.Co
SystemLabel SR.Co

NumberOfAtoms   131
NumberOfSpecies2

%block ChemicalSpeciesLabel
  1   6  C
  2   27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize  SZP
PAO.EnergyShift  0.05 Ry
PAO.SplitNorm0.2

==
==
# K-points

%block kgrid_Monkhorst_Pack
   1   0   0  0.0
   0   1   0  0.0
   0   0   1  0.5
%endblock Kgrid_Monkhorst_Pack
==
==
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
17.016 0.000 0.000
0.000 9.824 0.000
0.000 0. 14.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies

0.000 0.000 0.000 1
1.418 0.000 0.000 1
2.127 1.228 0.000 1
3.545 1.228 0.000 1
4.254 0.000 0.000 1
5.672 0.000 0.000 1
6.381  1.228 0.000 1
7.799  1.228 0.000 1
8.508  0.000 0.000 1
9.926  0.000 0.000 1
10.635 1.228 0.000 1
12.053 1.228 0.000 1
12.762 0.000 0.000 1
14.180 0.000 0.000 1
14.889 1.228 0.000 1
16.304 1.228 0.000 1
0.000  2.456 0.000 1
1.418  2.456 0.000 1
2.127  3.684 0.000 1
3.545  3.684 0.000 1
4.254  2.456 0.000 1
5.672  2.456 0.000 1
6.381  3.684 0.000 1
7.799  3.684 0.000 1
8.508  2.456 0.000 1
9.926  2.456 0.000 1
10.635 3.684 0.000 1
12.053 3.684 0.000 1
12.762 2.456 0.000 1
14.180 2.456 0.000 1
14.889 3.684 0.000 1
16.307 3.684 0.000 1
0.000  4.912 0.000 1

Re: [SIESTA-L] Transiesta DM does not converge

2020-06-17 Por tôpico Nick Papior 
Hi,

Den tir. 16. jun. 2020 kl. 22.00 skrev Seyed Mohammad Tabatabaei <
smt...@gmail.com>:

> Thank you so much for your answer.
>
> Do I need to use more buffer layers?
>
Maybe, first change to metallic MoS2, then see.

>
> I am currently using semiconducting MoS2 nanoribbons (1D system) with a
> bandgap of about 0.5 eV. Would changing to metallic MoS2 nanoribbons
> improve convergence?
>
Yes, using metallic electrodes would definitely help.

>
> Do you mean I should increase the cutt-off energy?
>
I didn't realize it was a nanoribbon. So no need for k-point convergence.
But you should converge system parameters before doing NEGF calculations.
This includes basis set optimization + mesh-cutoff etc.

>
>
>
>
>
> On Tue, Jun 16, 2020 at 12:36 AM Nick Papior  wrote:
>
>> Hi,
>>
>> 1. Great that you are using buffer atoms to get the *correct* behaviour
>> of your electrodes
>> 2. However, you are using MoS2 as electrodes, which is semiconducting.
>> This is not a good idea since the NEGF formalism requires the electrodes
>> are *bulk-like* and this cannot be enforced if the screening distance is
>> very long. This is the case for semi-conducting electrodes.
>> 3. Your other convergence parameters are very low, you really should
>> first converge the basic MoS2 setup for k-points, mesh-cutoff etc. but in
>> general, if you have semi-conducting electrodes, you shouldn't use NEGF
>> unless you are being really careful. :)
>>
>> Den lør. 13. jun. 2020 kl. 22.00 skrev Seyed Mohammad Tabatabaei <
>> smt...@gmail.com>:
>>
>>> Dear all,
>>>
>>> I am doing a TranSIESTA calculation for the following system.
>>>
>>> [image: image.png]
>>>
>>> However, I cannot converge the density matrix no matter how small my
>>> mixing weight is.
>>>
>>> I would be grateful if you help me with it. My output file is also
>>> attached.
>>>
>>> Best regards,
>>>
>>>
>>>
>>> --
>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>> --
>> SIESTA is supported by the Spanish Research Agency (AEI) and by the
>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 
Kind regards Nick

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)