[SIESTA-L] Macroave

2018-05-22 Por tôpico Seyed Mohammad Tabatabaei
Dear all,

I want to use the Macroave package for nonorhorhombic unit cells. As you
may know the version distributed with siesta only supports orthorhombic
cells. Does anyone know how should I adapt the code for nonorthorhombic
cells? Has anyone done this before?

Bests,
Mohammad,


Re: [SIESTA-L] problem in SCF convergence in transiesta run at higher bias points

2018-05-22 Por tôpico Leonardo Fonseca
The first steps to try are:

1) Use your 0.8 V output as starting point for your 1.2 V calculation
2) Lower your mixing parameters

If none of those help, try a smaller step, say going from 0.8 V to 1.0 V,
and then from 1.0 V to 1.2 V

2018-05-21 8:56 GMT-03:00 Bibhas Manna :

> Dear Siesta users,
>
> I am using transiesta code to get the I-V characteristics of a 2D
> structure (defected AGNR sheet). All the calculations (electrode,
> transiesta and tbtrans) run perfectly for some lower values of applied
> voltages (0.0 V, 0.4 V and 0.8 V) but a problem regarding SCF convergence
> arises for 1.2 V.
>
> I searched the siesta mail list for the solution and accordingly I changed
> my bias value for 1.2 V to 1.21 V but the problem persists.
>
>
> Could anyone suggest me why this is happening and how can I solve it even
> for other higher bias points??
>
> I am eagerly waiting for your kind reply.
>
>
> Thanking you.
> With regards,
>
> Bibhas Manna
> Research Scholar
> IIT Kharagpur
> India
>
>
>
>
>


Re: [SIESTA-L] problem in SCF convergence in transiesta run at higher bias points

2018-05-22 Por tôpico Nick Papior
There is nothing but trial and error for high bias calculations (and in
particular any transiesta calculation).
It isn't given that it will converge at all bias'.

Play with convergence parameters as usual.

2018-05-21 13:56 GMT+02:00 Bibhas Manna :

> Dear Siesta users,
>
> I am using transiesta code to get the I-V characteristics of a 2D
> structure (defected AGNR sheet). All the calculations (electrode,
> transiesta and tbtrans) run perfectly for some lower values of applied
> voltages (0.0 V, 0.4 V and 0.8 V) but a problem regarding SCF convergence
> arises for 1.2 V.
>
> I searched the siesta mail list for the solution and accordingly I changed
> my bias value for 1.2 V to 1.21 V but the problem persists.
>
>
> Could anyone suggest me why this is happening and how can I solve it even
> for other higher bias points??
>
> I am eagerly waiting for your kind reply.
>
>
> Thanking you.
> With regards,
>
> Bibhas Manna
> Research Scholar
> IIT Kharagpur
> India
>
>
>
>
>


-- 
Kind regards Nick


Re: [SIESTA-L] optimisation monoclinic to orthorhombic

2018-05-22 Por tôpico T. Liu
I tried increasing k-points to 4,6, and 8, but the results is similar, 
monoclinic structure changed to orthorhombic one. I will try to look 
into pseudopotential for oxygen.


Thanks,
Tao

On 2018-05-17 10:23, T. Liu wrote:

Dear all,

I made a test on CuO (monoclinic beta = 99 expt.), it accomplished but
the structure changed into an orthorhombic one (beta = 90). Does it
mean that the pseudopotential or/and basis set of Cu has some problems
or anything else? I also tried use 3p of Cu as semicore, but it goes
to beta=90 or SCF doesn't converge.
Thanks.

SystemName  CuO
SystemLabel CuO

NumberOfSpecies 2
NumberOfAtoms 8

%block ChemicalSpeciesLabel
1  29  Cu
2   8  O
%endblock ChemicalSpeciesLabel

LatticeConstant 1.0 Ang

%block LatticeVectors
4.6529998779 0.00 0.00
0.00 3.410858 0.00
   -0.8413048067 0.00 5.0382405853
%endblock LatticeVectors

AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
 0.25000 0.25000 0.0 1
 0.75000 0.75017 0.0 1
 0.75000 0.25000 0.49985 1
 0.25000 0.75017 0.49985 1
 0.0 0.41598 0.24992 2
 0.0 0.58402 0.74977 2
 0.5 0.91633 0.24992 2
 0.5 0.08393 0.74977 2
%endblock AtomicCoordinatesAndAtomicSpecies

MeshCutoff 800 Ry

MD.VariableCell  T

DM.Tolerance   0.10E-04
MD.MaxForceTol 0.001 eV/Ang
MD.MaxStressTol 0.01 GPa

XC.Functional GGA
XC.authors PBEsol

MaxSCFIterations 300 # Default value
SCFMustConverge T# Default value

PAO.BasisSize TZP

MD.TypeOfRunCG
MD.NumCGsteps   200
MD.VariableCell  T
DM.MixingWeight 0.15

%block kgrid_Monkhorst_Pack
2   0   0  0.5
0   2   0  0.5
0   0   2  0.5
%endblock kgrid_Monkhorst_Pack


Regards,
Tao


[SIESTA-L] Macroave for nonorthorhombic supercells

2018-05-22 Por tôpico Seyed Mohammad Tabatabaei
Dear all,

I have done all my heavy and time-consuming SIESTA calculations using big
hexagonal supercells and now I want to calculate the workfunctions of my
systems using SIESTA. My systems consist of the adsorption of different
molecules on graphene surface.

Reading the MACROAVE documentation, I found that it does not support
non-ortho-rhombic cells. So my question is:

Is it possible to change my final relaxed supercells to orthorhombic ones
and then use MACROAVE without any relaxation? As you know, graphene can
both have a rectangular and hegagonal unitcell, so it may be possible to
change the supercells such that they become orthorhombic. In this process,
the number of atoms in the supercells increases and there may be other
modifications but the overall physical picture would not change. Any
thoughts on the feasibility of this idea are welcome.

Bests,
Mohammad,


Re: [SIESTA-L] transport for 2D materials

2018-05-22 Por tôpico Nick Papior
2018-05-21 2:25 GMT+02:00 Zara Nosh :

> Dear Nick,
>
> Thank you very much for your response.
>
> So how should we study the transport properties of the pristine system
> under bias?
>
It is an unphysical system if you are studying a pristine system with
applied bias. For exactly the reason you see in your initial question. The
junction only has the potential drop across the full system length, in
which case the system is length dependent (which it shouldn't).

> Maybe just by considering the zero-bias transmission; but in this regards,
> we cannot find for example NDR characteristic of a system.
>
> Regards,
> Zara
>
> On Sun, May 20, 2018 at 12:18 PM, Nick Papior 
> wrote:
>
>> Dear Zara,
>>
>> On Sat, 19 May 2018, 22:03 Zara Nosh,  wrote:
>>
>>> Dear expert,
>>>
>>> My results show that calculating the current under bias voltage in a
>>> pure 2D system depends on the length of scattering region. Also, this
>>> dependent is not linear, for example, under bias voltage 2V the calculated
>>> current in the larger system is 1/3 of the current of the smaller system
>>> but under bias voltage 3 this ratio could be different.
>>>
>>> As the system is pure and there is no scatterer in the system, what is
>>> the reason of this behavior?
>>>
>> Because simulating a pristine system with bias is physically wrong.
>>
>>>
>>> Second question: is transiesta method valid for such a study
>>> (calculating current under bias-voltage in  a 2D system)?
>>>
>> Transiesta is valid for 2D systems. One cannot apply bias to pristine
>> systems, but otherwise you can.
>>
>>>
>>> I really appreciate your help in advance.
>>>
>>> Best regards,
>>> Zara
>>>
>>
>


-- 
Kind regards Nick