Dear siesta users,
I'm dealing with a convergence problem on a slab system (gamma-maghemite).
Everything works fine for the bulk, I could optimized the atomic positions
as well as the cell parameters. Also, I computed the DOS giving the
expected one. But when I add a vacuum region I have a diverge
Dear Siesta users
I am doing transport calculation using
transiesta package implemented in siesta 4.0 version. Generally I see that
as we apply higher bias voltage between the electrodes, then it becomes
difficult to converge. Can anyone please tell me some general met
Hi all
I was running a calculation for a molecular junction device in
transiesta. In siesta calculation, it got converged but in transiesta
calculation, it's not converging. Can anyone please help me asap. For your
convenience, I am attaching the input file here. Should I change any
paramet
Hello Rupesh
This is a trial and error situation
So I’m other words if 0.5 V did not work try 0.501 0.503 V because I had
similar issues and it worked when I changed a bit the voltage.
Hope that works and Good luck !
El abed
Sent from my iPhone
On 6 Nov 2019, at 8:02 am, RUPESH TIWARI
mailto:ru
Dear SIESTA Team,
Recently I have performed computations for polycyclic aromatic
hydrocarbons. I have tried different default basis sets. As a result, I
have pretty good results fro SZP set - it turns out this basis set works
much better than TZTP. That seems strange for me since I expected a
conv
Dear Siesta users,
I have been trying to optimize a 32 atom 2D supercell of Germanium Carbide.
For that I am trying to test the convergence of my system with respect to
the k-mesh value. Following according to the siesta hands on tutorial, I
have run optimization of the system with k-mesh value st
Dear all
During mesh cutoff convergence study for graphene I am using 0.01 eV as a
convergence criteria.
Is that ok?
please guide me.
Thank u
Regards
Riya
Dear Rajan,
thanks for this information. I will in future work with this procedure.
Some more things that confuse me are the following:
1. When I re-run the same setup, I get deviations up to 15% in the
transmission. What could be the reason for this?
2. I did calculations of the same setup wi
Your electrodes may be erroneously setup.
I encourage you to check the electronic structure (ES) of something
you already know the result of.
If you can't reproduce such an ES you may question your compilation.
2016-03-17 13:45 GMT+01:00 :
> Dear Rajan,
>
> thanks for this information. I will in
Hii
You should do following steps:
1. Decide your structure
2. Run structure with different k pts and plot energy vs k pt
See after some k pt energy values nearly same
3. Do same with mesh cuttoff
4. Relax structure with CG steps
5. Then electrode calculation
And finally tranmission calculation
Dear users,
I am pretty new to Siesta/TranSiesta and I'm currently struggling with the
following topic: I want to compute equilibrium transmission of
Poly(3-Methylthiophene) with different chain lengths. My current (ideally
periodic) _test_ system consists of 100 atoms (a 10mer) of which 2x40 a
Dear Dr. Papior,
Thanks so much for your reply.
Must I do the energy convergence test?
Thanks in advance,
Best regards.
Nadia Salami
On Fri, Jul 3, 2015 at 11:58 AM, Nick Papior wrote:
> As you said, convergence tests is the way to go.
>
> 2015-07-03 9:06 GMT+02:00 Nadia Salami :
>
>> Dear Dr.
As you said, convergence tests is the way to go.
2015-07-03 9:06 GMT+02:00 Nadia Salami :
> Dear Dr. Papior,
>
> Thank you very much for your reply.
> I have applied these options,
>
> TS.BiasContour.Eta 0.0001 Ry
> TS.BiasContour.NumPoints 10
>
> But I don't know how to obtain the optimi
Dear Dr. Papior,
Thank you very much for your reply.
I have applied these options,
TS.BiasContour.Eta 0.0001 Ry
TS.BiasContour.NumPoints 10
But I don't know how to obtain the optimized value.
Your Guidance will be highly appreciated.
Thanks a lot.
Best,
Nadia Salami
On Fri, Jul 3, 2015
Please read the documentation for transiesta.
In the currently released versions these keywords should peak your interest:
TS.BiasContour.Eta
TS.BiasContour.NumPoints
2015-07-03 5:33 GMT+02:00 Nadia Salami :
> Dear Transiesta users,
>
> According to DOI: 10.1103/PhysRevB.65.165401, I know that
Dear Transiesta users,
According to DOI: 10.1103/PhysRevB.65.165401, I know that the
non-equilibrium part of density matrix must be evaluated for a finite level
broadening and on a fine grid. I need to do convergence test in the level
broadening and number of grid points. But I don't know how to d
It's in French.
Best wishes, Maxim.
2014-07-26 17:36 GMT+04:00 邵德喜 :
> Thanks very much.Is it Spanish? I can't understant it ,but I 'll try my
> best to catch it .
> Dexi Shao
>
>
> 2014-07-26 21:24 GMT+08:00 Максим Арсентьев :
>
> more easily to take only max force for plot from output. See pag
Thanks very much.Is it Spanish? I can't understant it ,but I 'll try my
best to catch it .
Dexi Shao
2014-07-26 21:24 GMT+08:00 Максим Арсентьев :
> more easily to take only max force for plot from output. See pages 79-80
> of file attached - it can help you to choose these parameters
>
>
> 2014
it is *.FA file contains forces (eV/Ang)
Best wishe, Maxim.
2014-07-26 17:00 GMT+04:00 邵德喜 :
> Dear Maxim:
> I'm so sorry to disturb you again,but I've completed the kpoint grid
> convergence with a reletive high value of Meshcutoff just follow your
> words.Then I've got many FORCE_STRESS f
Dear Maxim:
I'm so sorry to disturb you again,but I've completed the kpoint grid
convergence with a reletive high value of Meshcutoff just follow your
words.Then I've got many FORCE_STRESS files related to different kpoint
grid.In these files the first four lines is just as follows：
Thanks very very much for all your replay,saluted all of you !
Dexi Shao
2014-07-25 19:22 GMT+08:00 Максим Арсентьев :
> Yes, you right.
> To clarify 1st keep fixed high meshcutoff and vary kpoint -> select kpoint
> and keep it fixed but vary meshcutoff
> Maybe this can be vice versa, or not,bu
Yes, you right.
To clarify 1st keep fixed high meshcutoff and vary kpoint -> select kpoint
and keep it fixed but vary meshcutoff
Maybe this can be vice versa, or not,but possibly it is not so important
(final value of meshcutoff about 350-400 Ry, sometimes for late heavy
transition metal elements,
I see.You mean that I should set CG steps as usual as we do structual
relaxation(foer example :500) during all the convergence tests .
And consider kpoint grid convergence first with a reletive high value of
Meshcutoff.When it is done ,plot how it depends on FORCES from
the output file in the fin
Dear Dexi!
You should not set nember of CG steps to zero - it is not necessary. You
right that you should perform convergence of your property of interest, but
first structural relaxation is important as I suppose - maybe not in your
case, but often it is so. So select high meshcutoff about 400-50
Thanks very much.The unit is Ry.
I was told that when I get the original structure ,I should do convergence
tests first,structual relaxation comes second.
In my opinion ,do convergence test without structual relaxation I should
set CG step to zero.
problem1:I check the convergency (in terms of grad
Dear Dexi,
I wonder what is the unit of your Mesh cutoff? Is it in Ry?
Siesta is using atomic orbital as the basis, which is quite different from
plane-wave based codes like VASP. In plane-wave code, the plane wave cutoff
energy directly determines your basis, and thus influences the result a lot
Dear everyone:
I have done the convergence test when I check the convergency (in terms of
gradually increase Meshcutoff) of the total energy, I found that the Total
energy rise up when I increase the parameter of Meshcutoff (please refer to
the accesory) .Is it reasonable?
Ahy replay will be appr
On 12/19/13, Suman Chowdhury wrote:
> Dear all siesta user,
> How do I know if my molecular dynamics simulation is converging or not?
>
Hi dear Suman
when you face with outcoor: Relaxedatomic coordinates
(Ang).in your output file.
Dear all siesta user,
How do I know if my molecular dynamics simulation is converging or not?
ms I set it to 0.0008 and then restart from that
>>> DM
>>> >>>> file with a stringer convergence criterion.
>>> >>>>
>>> >>>> Here is the settings I am using for my calculations:
>>> >>>>
>>> >>>>
>>>> difference
> >>>> DM.UseSaveDM.false. # to use
> continuation
> >>>> files
> >>>>
> >>>> DM.NumberKick 100
> >
>> >>>> for grid
>> >>>>
>> >>>>
>> >>>> MaxSCFIterations250 # Maximum number of SCF
>> >>>> iter
>> >>>> DM.NumberBroyden3
>> >>>>
s250 # Maximum number of SCF
> >>>> iter
> >>>> DM.NumberBroyden3
> >>>> DM.MixingWeight 0.01 # New DM amount for next
> >>>> SCF cycle
> >>>> DM.Tolerance
ation
>>>> files
>>>>
>>>> DM.NumberKick 100
>>>> DM.KickMixingWeight0.01
>>>> #--
>>>>
>>>> Suerte!
>>>>
>>>> P
.@gmail.com>
<mailto:ars21031...@gmail.com
<mailto:ars21031...@gmail.com>>__]
*Sent:*Wednesday, November 20, 2013 7:29 AM
*To:*siesta-l@uam.es <mailto:siesta-l@uam.es>
<mailto:siesta-l@uam.es <mailto:siesta-l@u
gt;>
>>> Suerte!
>>>
>>> PS: yo tambien soy caleña!
>>>
>>> Diana M. Otálvaro
>>> PhD Candidate
>>>
>>> Computational Material Science
>>> MESA+ Institute of Nanotechnology
>>>
uam.es <mailto:siesta-l-requ...@uam.es>
[siesta-l-requ...@uam.es <mailto:siesta-l-requ...@uam.es>] on
behalf of Максим Арсентьев [ars21031...@gmail.com
<mailto:ars21031...@gmail.com>]
*Sent:*Wednesday, November 20, 2013 7:29 AM
*To:*siesta-l@uam.es <mailto:siesta-l@
notechnology
> University of Twente.
> Enschede, Nederland
> --
> *From:* siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] on behalf of
> Максим Арсентьев [ars21031...@gmail.com]
> *Sent:* Wednesday, November 20, 2013 7:29 AM
> *To:* siesta-l@uam
hede, Nederland
> From: siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] on behalf of Максим
> Арсентьев [ars21031...@gmail.com]
> Sent: Wednesday, November 20, 2013 7:29 AM
> To: siesta-l@uam.es
> Subject: Re: [SIESTA-L] Convergence problem on heterostructure.
>
> I forg
Dear Maxim,
I'd like to ask you something about your simulation. It turns out that when I
do a geometry optimisation, I don't get convergence for the values of energy in
the self consistent cycle. When you performed your simulation, did the values
of energy converged for every MD step, or did t
wente.
Enschede, Nederland
From: siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] on behalf of Максим
Арсентьев [ars21031...@gmail.com]
Sent: Wednesday, November 20, 2013 7:29 AM
To: siesta-l@uam.es
Subject: Re: [SIESTA-L] Convergence problem on heterostructur
I forgot to tell you - besides DM.MixingWeight 0.05 I also set
PAO.EnergyShift to 65 meV as here
http://www.nature.com/nnano/journal/v7/n9/extref/nnano.2012.127-s2.txt .
Best wishes,
Dr. Maxim Arsent'ev
Laboratory of inorganic synthesis
Institute of Silicate Chemistry of RAS
2013/11/18 Mahmoud H
You could also try to increase the non-equilibrium contour points.
Mahmoud
On Nov 18, 2013, at 11:22, "Sebasti?n Cauce do D?vila"
mailto:sebastian.caic...@correounivalle.edu.co>>
wrote:
Thank you very much for your suggestion. I will give it a try!
Sebasti?n Caicedo D?vila
Bionanoelectronics
Thank you very much for your suggestion. I will give it a try!
Sebastián Caicedo Dávila
Bionanoelectronics research group
School of electrical and electronics engineering
Universidad del Valle
Cali - Colombia
> On 18/11/2013, at 11:50, Максим Арсентьев wrote:
>
> I also try some siesta only si
I also try some siesta only six months, but for a more heterogeneous
structure I noticed that the reduction DM.MixingWeight reduces oscillations
in convergence, so try to play with it (decrease DM.MixingWeight). See
http://www.nature.com/nnano/journal/v7/n9/extref/nnano.2012.127-s2.txt
Maybe someon
First of all thank you very much for the suggestions, now I can reach
convegence quite easily.
The results should be correct: I have compared them with other calculations
and for example the, charged, relaxed configurations are the same as those
obtained
with other meathods that I know are right.
B
Dear Luigi,
Si5H12 has an even number of electrons, therefore
when adding or removing one, in principle, you ought to use
spin polarized = true.
(This will become less and less crucial as you increase
the system so it becomes more "solid-like" and/or metallic.
But at the beginning this extra elect
Dear Luigi,
Si5H12 has an even number of electrons, therefore
when adding or removing one, in principle, you ought to use
spin polarized = true.
(This will become less and less crucial as you increase
the system so it becomes more "solid-like" and/or metallic.
But at the beginning this extra elect
Dear Abraham,
first of all thank you very much for your reply, it was very usefull and I
was able to make my small test calculations converge.
But now I moved to larger systems and I get very anoying runtime errors
that make my calculations crash.
The runtime errors I get are the following:
forrtl
Hi Luigi,
A few suggestions:
1) Your MaxCGsteps and MaxSCFIterations are both very large, convergence in
many problems can be adequately approached by using a small number of CG
updates, like 10-50 to perform a stepwise convergence, changing mixing
parameters slightly between runs, observing how
Hello everybody,
I am trying to perform a calculation of a charged system composed of a
molecule of Si5H12
with an extra electron (and in the future also one less electron) so I set:
NetCharge -1.00
SpinPolarized .true.
FixSpin .true.
TotalSpin 1.0
Bu
Hi Gregorio
you don't have any problem in the run, this unusual because of the large
number of atoms in addition you calculated optical properties and band
structure at the same time this requires a great time
On Thu, Nov 22, 2012 at 3:54 PM, Gregorio García Moreno
wrote:
> The optimization is ru
The optimization is running (I don't know slowly or quickly, it's depends).
Note, the max atomic forces and siesta E_KS energy decrease as a
function of cycles number (although there is some increases).
I think it's ok (I didn't see the optimization parameters. But I think
you are using a high
Hello, all
I am doing a geometry optimization of graphene which is passivated with
Hydrogen atoms at the edge of the sheet, and a Hydrogen atom is adsorbed on the
top of a carbon atom in the center of the grapheme layer. In the calculation,
the convergence criterion is MD.MaxforceTol = 0.01
Hi,
You might also try the Broyden method, which by default operates with
a self-adjusting mixing weight. Check the manual.
Best,
Roberto
On Fri, 10 Aug 2012, shihitwh wrote:
Hi, Diana
You can try to change the parameters
DM.MixingWeight
DM.NumberPulay .
Best Wishes!
Hi, Diana
You can try to change the parameters
DM.MixingWeight
DM.NumberPulay .
Best Wishes!
Shi
At 2012-04-24 02:41:07,"Diana Otalvaro" wrote:
>Hello everyone,
>
>
>I have a lot of problems converging the DM of a structure where I
Hello everyone,
I have a lot of problems converging the DM of a structure where I force
antiparallel magnetization in the two Ni leads, and have a scattering region
made of non-magnetic material. I force the AP magnetization by using %block
DM.InitSpin.
I wonder if the DM.Tolerance criterio
-- Forwarded message --
From: vaneeta bala
Date: Wed, Dec 14, 2011 at 10:36 AM
Subject: [SIESTA-L]
To: siesta-l@uam.es
Hi
i am trying to make 2 layers of Polyvinyl alcohol
its unit cell has 2 chains of [-CH2CHOH]i.e. 14 atoms using supercell(1 3
2) ,lattice parametre (7.83, 2.5
I am having the same problem. Could anybody please help us with these
problem..
On Tue, Nov 8, 2011 at 5:27 AM, Arunkumar C R wrote:
> Dear Siesta users,
>
> I was working with a metallic system 2u-5u-2u where u stands for the unit
> cell consisting of N atoms. Many attempts have been made to mak
Dear Siesta users,
I was working with a metallic system 2u-5u-2u where u stands for the unit
cell consisting of N atoms. Many attempts have been made to make my
transiesta run converged, but only siesta part does so. At this juncture,
I would like to intervene your attention towards my problem. T
Dear all,
as I know that calculations with metals can be quite ugly, I wanted to
ask if there are metals which are a bit nicer in convergence behavior?
To be more precise I can choose between Cu, Co, Ni, Mo and Pd.
Are there any suggestions of elements I should try to avoid for now. A
collea
Humanity is Service to
God
---
--- On Thu, 9/30/10, Marcos Veríssimo Alves
wrote:
From: Marcos Veríssimo Alves
Subject: Re: [SIESTA-L] Convergence for large nanowires
To: siesta-l@uam.es
Date: Thursday, September 30, 2010, 11:08 AM
Pavan,
If I'm not mistaken there was a bug in the extrapolation of the DM in siesta
3.0-b - sometimes it would lead to such problems. However, I think this bug
has been fixed in the latest release candidates. If you don't wish to change
the version of Siesta, then you should disable the DM extrapo
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