Re: [SIESTA-L] Band structure for BiFeO3

[ionut ghitiu]

 Dear A. Postnikov,
Yes, the structure that I'm currently using is supposed to be antiferromagnetic 
and can be found here:mp-23501: FeBiO3 (trigonal, R3c, 161)


| 
| 
|  | 
mp-23501: FeBiO3 (trigonal, R3c, 161)

Browse many computed properties for this trigonal FeBiO3 compound, including 
formation energy from the elements,...
 |

 |

 |



Also I've uploaded on my drive two band structures with their respective PDOS 
from calculations that i tried, as I'm not sure how the mailing list treats 
attachments. One of them has the total magnetization imposed to be 0, the other 
one not, but both seem to be antiferromagnetic as Qtot(up)=Qtot(down)=49.Bands 
– Dysk Google


| 
| 
|  | 
Bands – Dysk Google


 |

 |

 |



You can see that my spin up and spin down energies are pretty much identical 
(they should be in orange and blue, but they just overlap giving a darker shade 
of orange), while on the materialsproject website there is quite a big 
difference between them (the general shape of the band structure being somewhat 
similar). Also my PDOS seems to look the same for the 2 spin orientations.
I am quite confused at what may be the cause of this problem.
Regards,Ioan Ghitiu


On Tuesday, February 9, 2021, 01:44:15 AM GMT+2, Andrei Postnikov 
 wrote:  
 
 #yiv2106717520 body 
{min-height:100%;color:#00;font-size:12pt;font-family:arial, helvetica, 
sans-serif;}Dear ionutghitiu,your message is a bit confusing. You say your band 
structures are like in other calculations,the magnetic moments are like in the 
literature - what is the problem, then?The list of different parameters you 
tried is impressive but doesn't give a clue.You have large Fe magnetic moments 
but you see no spin splitting in (total?) DOS and bands -are you looking at an 
antiferromagnetic solution? 
Best regards
Andrei Postnikov
- ionut ghitiu  a écrit :
>Dear Siesta users,
I've been trying to obtain the band structure of BiFeO3 for some time now, mind 
you it's my first project involving Siesta or dtf so please bear with me. The 
thing is, the band structures that I get are really similar to the ones from 
materialsproject for the same structure (I am using the R3C primitive cell) but 
for the fact that the system seems to be spin degenerate, and so I get no 
splitting of the bands or difference in DOS. 
To give you some details about the system, I'm currently using FR/SR 
pseudopotentials from Pseudo-Dojo and an optimized base, but I also tried with 
the default one (up to TZDP i think). My MeshCutoff usually was 250 Ry, but 
recently changed it to 350 Ry, and I also had a FilterCutoff of 200-250 Ry. 
Also, I've been using a 5x5x5 gamma-centered kgrid and moved to a 7x7x7 . I'm 
initializing the Spin as polarised and setting the spins for the 2 Fe atoms as 
+/- (tried with values and with InitSpin.AF). As tolerances I use 1.d-5 for DM 
and the default one for HTol, but also tried with 1.d-6 for DM and 4.d-4 eV for 
the Hamiltonian. I tried both relaxed and unrelaxed systems. The thing is the 
magnetic moments written in the MullikenPop are close to what I've found in 
literature +-4.37 for Fe, 0.004 for Bi, and 0.029 for O.
Also, I've tried experimenting a little on Fe2O3 with the same R3C structure 
and have the same problem, while on NiO everything went well. For Fe I'm using 
3s2, 3p6, 3d6 and 4s2 electrons for the base.
Could you please give me any hints on what I'm doing wrong or what to try next? 
I feel like I'm going in circles. Thanks a lot!
  
-- 
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] Band structure for BiFeO3

[Andrei Postnikov]

Dear ionutghitiu,your message is a bit confusing. You say your band structures 
are like in other calculations,the magnetic moments are like in the literature 
- what is the problem, then?The list of different parameters you tried is 
impressive but doesn't give a clue.You have large Fe magnetic moments but you 
see no spin splitting in (total?) DOS and bands -are you looking at an 
antiferromagnetic solution? Best regardsAndrei Postnikov
- ionut ghitiu  a écrit :
>Dear Siesta users,
I've been trying to obtain the band structure of BiFeO3 for some time now, mind 
you it's my first project involving Siesta or dtf so please bear with me. The 
thing is, the band structures that I get are really similar to the ones from 
materialsproject for the same structure (I am using the R3C primitive cell) but 
for the fact that the system seems to be spin degenerate, and so I get no 
splitting of the bands or difference in DOS. 
To give you some details about the system, I'm currently using FR/SR 
pseudopotentials from Pseudo-Dojo and an optimized base, but I also tried with 
the default one (up to TZDP i think). My MeshCutoff usually was 250 Ry, but 
recently changed it to 350 Ry, and I also had a FilterCutoff of 200-250 Ry. 
Also, I've been using a 5x5x5 gamma-centered kgrid and moved to a 7x7x7 . I'm 
initializing the Spin as polarised and setting the spins for the 2 Fe atoms as 
+/- (tried with values and with InitSpin.AF). As tolerances I use 1.d-5 for DM 
and the default one for HTol, but also tried with 1.d-6 for DM and 4.d-4 eV for 
the Hamiltonian. I tried both relaxed and unrelaxed systems. The thing is the 
magnetic moments written in the MullikenPop are close to what I've found in 
literature +-4.37 for Fe, 0.004 for Bi, and 0.029 for O.
Also, I've tried experimenting a little on Fe2O3 with the same R3C structure 
and have the same problem, while on NiO everything went well. For Fe I'm using 
3s2, 3p6, 3d6 and 4s2 electrons for the base.
Could you please give me any hints on what I'm doing wrong or what to try next? 
I feel like I'm going in circles. Thanks a lot!

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

[SIESTA-L] Band structure for BiFeO3

[ionut ghitiu]

Dear Siesta users,
I've been trying to obtain the band structure of BiFeO3 for some time now, mind 
you it's my first project involving Siesta or dtf so please bear with me. The 
thing is, the band structures that I get are really similar to the ones from 
materialsproject for the same structure (I am using the R3C primitive cell) but 
for the fact that the system seems to be spin degenerate, and so I get no 
splitting of the bands or difference in DOS. 
To give you some details about the system, I'm currently using FR/SR 
pseudopotentials from Pseudo-Dojo and an optimized base, but I also tried with 
the default one (up to TZDP i think). My MeshCutoff usually was 250 Ry, but 
recently changed it to 350 Ry, and I also had a FilterCutoff of 200-250 Ry. 
Also, I've been using a 5x5x5 gamma-centered kgrid and moved to a 7x7x7 . I'm 
initializing the Spin as polarised and setting the spins for the 2 Fe atoms as 
+/- (tried with values and with InitSpin.AF). As tolerances I use 1.d-5 for DM 
and the default one for HTol, but also tried with 1.d-6 for DM and 4.d-4 eV for 
the Hamiltonian. I tried both relaxed and unrelaxed systems. The thing is the 
magnetic moments written in the MullikenPop are close to what I've found in 
literature +-4.37 for Fe, 0.004 for Bi, and 0.029 for O.
Also, I've tried experimenting a little on Fe2O3 with the same R3C structure 
and have the same problem, while on NiO everything went well. For Fe I'm using 
3s2, 3p6, 3d6 and 4s2 electrons for the base.
Could you please give me any hints on what I'm doing wrong or what to try next? 
I feel like I'm going in circles. Thanks a lot!

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

[SIESTA-L] band structure and PDOS of the central molecule of device

[ANKITA JOSHI]

Dear SIESTA users,

I want to determine band structure and PDOS of only central molecule in a
device. Does anyone know how to make the input files? Please give any
suggestions.

Thanks
Ankita

Re: [SIESTA-L] Band structure calculations

[Nick Papior]

Band-structures are typically a quantity that is of interest in the minimal
unit-cell representation of the electrodes, and/or the periodic minimal
part of the scattering region.

The bandstructure of the full device is somewhat difficult to interpret.

Den fre. 24. aug. 2018 kl. 22.13 skrev ANKITA JOSHI :

> Dear SIESTA users,
>
> I am bit confused regarding the band structure calculations. The procedure
> followed to calculate band structure is:
>
> 1. First I did full relaxation of the system electrode-molecule-electrode.
> 2. Then, using the optimized coordinates of the system
> electrode-molecule-molecule, I have done the band structure calculations.
>
> Is this the correct approach? Also, how to do the band structure
> calculation only for the scattering region?
>
> Thanks
> Ankita
>


-- 
Kind regards Nick

[SIESTA-L] Band structure calculations

[ANKITA JOSHI]

Dear SIESTA users,

I am bit confused regarding the band structure calculations. The procedure
followed to calculate band structure is:

1. First I did full relaxation of the system electrode-molecule-electrode.
2. Then, using the optimized coordinates of the system
electrode-molecule-molecule, I have done the band structure calculations.

Is this the correct approach? Also, how to do the band structure
calculation only for the scattering region?

Thanks
Ankita

Re[2]: [SIESTA-L] Band structure (Silver)

[Mehdi Shamekhi]

Choose the minimum number of atoms which you can build your whole structure 
based on lattice vectors. For example the unit cell of graphene in consist of 4 
or 2 atoms, phosphorene is 4 and etc
Based on your unit cell and the lattice constants calculate the reciprocal 
vectors. 
Draw your structure based on your reciprocal vectors and try to calculate the 
(x,y) of the edges. They will be M,K,S,Y 
THE (x,y) will be in your bandline block.
Regards,
Mehdi

___
Mehdi Shamekhi
MSc student of Electrical Engineering
Department of Electrical Engineering
University of Zanjan, Zanjan, Iran
On Sun, Jun 24, 2018 at 00:36, Dinesh Thapa  wrote: 
Dear Nick,
I appreciate for your suggestions. I still get confused as you said that i am 
not calculating minimal Ag unit cell. What does it mean ? Since i took Ag-FCC 
structure as unit cell. Also, How could i get vertical lines and its label like 
K, L, M ... as high symmetric points in Band structure plot.
sincerely,
Dinesh
On Thu, Jun 21, 2018 at 3:14 PM, Nick Papior  wrote:

In seems you need to do multiple things differently :1) too low mesh cutoff 2) 
you need to sample the brilloun zone sufficiently3) you are not calculating the 
minimal Ag unit cell
The first two you need to converge sufficiently. Check the manual for details. 

--

Kind regards Nick Papior
On Thu, 21 Jun 2018, 22:00 Dinesh Thapa,  wrote:

I tried to Plot band structure for Silver (Ag) using SIESTA But i am not 
getting good plot as that of VASP. Also, i could not get vertical lines on the 
particular high symmetric points. I tried to ayttach my input.fdf and JPEG of 
Band structure. Any body;s help in this is highly appreciated.
with regards
Dinesh

Re: [SIESTA-L] Band structure (Silver)

[Dinesh Thapa]

Dear Nick,
I appreciate for your suggestions. I still get confused as you said that i
am not calculating minimal Ag unit cell. What does it mean ? Since i took
Ag-FCC structure as unit cell. Also, How could i get vertical lines and its
label like K, L, M ... as high symmetric points in Band structure plot.
sincerely,
Dinesh


On Thu, Jun 21, 2018 at 3:14 PM, Nick Papior  wrote:

> In seems you need to do multiple things differently :
> 1) too low mesh cutoff
> 2) you need to sample the brilloun zone sufficiently
> 3) you are not calculating the minimal Ag unit cell
>
> The first two you need to converge sufficiently. Check the manual for
> details.
>
>
> --
>
> Kind regards Nick Papior
>
>
> On Thu, 21 Jun 2018, 22:00 Dinesh Thapa,  wrote:
>
>> I tried to Plot band structure for Silver (Ag) using SIESTA But i am not
>> getting good plot as that of VASP. Also, i could not get vertical lines on
>> the particular high symmetric points. I tried to ayttach my input.fdf and
>> JPEG of Band structure. Any body;s help in this is highly appreciated.
>>
>> with regards
>> Dinesh
>>
>

Re: [SIESTA-L] Band structure (Silver)

[Nick Papior]

In seems you need to do multiple things differently :
1) too low mesh cutoff
2) you need to sample the brilloun zone sufficiently
3) you are not calculating the minimal Ag unit cell

The first two you need to converge sufficiently. Check the manual for
details.


--

Kind regards Nick Papior


On Thu, 21 Jun 2018, 22:00 Dinesh Thapa,  wrote:

> I tried to Plot band structure for Silver (Ag) using SIESTA But i am not
> getting good plot as that of VASP. Also, i could not get vertical lines on
> the particular high symmetric points. I tried to ayttach my input.fdf and
> JPEG of Band structure. Any body;s help in this is highly appreciated.
>
> with regards
> Dinesh
>

[SIESTA-L] Band structure (Silver)

[Dinesh Thapa]

I tried to Plot band structure for Silver (Ag) using SIESTA But i am not
getting good plot as that of VASP. Also, i could not get vertical lines on
the particular high symmetric points. I tried to ayttach my input.fdf and
JPEG of Band structure. Any body;s help in this is highly appreciated.

with regards
Dinesh


ag.fdf
Description: Binary data

Re: [SIESTA-L] Band structure

[Kamaraj M]

Dear Dinesh,

Please search the archives, at least make an attempt to search the
available documentation, you will get more information.  As a beginner, it
is advisable to search the available tutorials. You may look at the below
link. It may help you.

1. https://departments.icmab.es/leem/siesta/tlv14/index.html
2.
http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Hands-on-session.html

With regards
kamaraj


On Tue, Jun 19, 2018 at 12:01 AM, Dinesh Thapa 
wrote:

> Being subscribed to SIESTA, I want to ask how can i correctly calculate
> charge density, DOS and band structure (with vertical lines in high
> symmetry KPOINTS). Since i am new in SIESTA.
>
> with regards,
> Dinesh Thapa
>



-- 

M.Kamaraj, CSIR-SRF
C/o Dr.V Subramanian FASc, FNASc,
Inorganic & Physical Chemistry Division
CSIR-Central Leather Research Institute,
Adyar, Chennai, India. 600 020.


http://clri.res.in/subramanian/index.html
https://scholar.google.co.in/citations?user=Jm-3d-YJ=en
https://www.researchgate.net/profile/Manoharan_Kamaraj

[SIESTA-L] Band structure

[Dinesh Thapa]

Being subscribed to SIESTA, I want to ask how can i correctly calculate
charge density, DOS and band structure (with vertical lines in high
symmetry KPOINTS). Since i am new in SIESTA.

with regards,
Dinesh Thapa

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Again thank you so so much Prof. Nick Papior

On Sun, Feb 4, 2018 at 11:44 PM, Nick Papior  wrote:

> I used PDOS from siesta, just as you said you did in your original post.
>
> 2018-02-04 17:25 GMT+01:00 Suman Chowdhury :
>
>> Just let me know how did you calculate the DOS..
>>
>> On Sat, Feb 3, 2018 at 3:04 AM, Nick Papior  wrote:
>>
>>> Dear Suman,
>>>
>>> I think you should solve this yourself.
>>>
>>> 2018-02-02 5:56 GMT+01:00 Suman Chowdhury :
>>>
 Dear Nick Papior,

 Thank you so so much for your help. Can you help me in this regard
 about how I can get the correct coordinates for plotting the band
 structure??

 On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior 
 wrote:

> If I run your system without performing cell relaxations I find the
> attached eigenvalues (for the Monkhorst-Pack grid).
>
> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
> cell-relaxation does not change the spectrum drastically then this is what
> you should suspect in the PDOS.
> Secondly, the PDOS is *exactly* reproducing the bandgab in this
> calculation.
>
> 1) I would highly suggest you to perform cell/coordinate relaxations
> in one directory, then afterwards perform analysis on the relaxed
> structure, PDOS, band-structure, optical, etc.
> 2) Possibly your band-structure coordinates are wrong because when I
> plot the bandstructure for this structure it does not capture the correct
> band gab (this *has* to be the problem).
>
> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury  >:
>
>> I have just tried to see the variation of TDOS by changing the
>> smearing parameter. But I could not observe any change in it.
>>
>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>> sumanchowdhur...@gmail.com> wrote:
>>
>>> This is the fdf that I have used...
>>>
>>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
>>> wrote:
>>>
 Dear Suman,

 Without data (plots) or fdf file it is very difficult to help you.
 It could be that your smearing parameter is too large.


 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <
 sumanchowdhur...@gmail.com>:

> Dear SIESTA User,
>
> Recently I am getting some confusing results by using SIESTA.
> While plotting a band structure I am getting a band gap which is quite
> large. However, when I am trying to plot its corresponding total 
> partial
> density of states (PDOS), I can clearly see that there is no 
> existence of
> any band gap. But interestingly the component PDOS are giving the 
> required
> band gap. The problem is with the total PDOS. Do any of you have any 
> idea
> about these kinds of results...
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
> 79, West Bengal, India.*
>
>


 --
 Kind regards Nick

>>>
>>>
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>>
>>>
>>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>> 79, West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



 --
 *Dr. Suman Chowdhury*



 *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232 <+91%2098305%2012232>*


>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Nick Papior]

I used PDOS from siesta, just as you said you did in your original post.

2018-02-04 17:25 GMT+01:00 Suman Chowdhury :

> Just let me know how did you calculate the DOS..
>
> On Sat, Feb 3, 2018 at 3:04 AM, Nick Papior  wrote:
>
>> Dear Suman,
>>
>> I think you should solve this yourself.
>>
>> 2018-02-02 5:56 GMT+01:00 Suman Chowdhury :
>>
>>> Dear Nick Papior,
>>>
>>> Thank you so so much for your help. Can you help me in this regard about
>>> how I can get the correct coordinates for plotting the band structure??
>>>
>>> On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior 
>>> wrote:
>>>
 If I run your system without performing cell relaxations I find the
 attached eigenvalues (for the Monkhorst-Pack grid).

 In this case there is *only* a bandgab of ~0.5 eV. Provided that the
 cell-relaxation does not change the spectrum drastically then this is what
 you should suspect in the PDOS.
 Secondly, the PDOS is *exactly* reproducing the bandgab in this
 calculation.

 1) I would highly suggest you to perform cell/coordinate relaxations in
 one directory, then afterwards perform analysis on the relaxed structure,
 PDOS, band-structure, optical, etc.
 2) Possibly your band-structure coordinates are wrong because when I
 plot the bandstructure for this structure it does not capture the correct
 band gab (this *has* to be the problem).

 2018-01-31 16:35 GMT+01:00 Suman Chowdhury 
 :

> I have just tried to see the variation of TDOS by changing the
> smearing parameter. But I could not observe any change in it.
>
> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
> sumanchowdhur...@gmail.com> wrote:
>
>> This is the fdf that I have used...
>>
>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
>> wrote:
>>
>>> Dear Suman,
>>>
>>> Without data (plots) or fdf file it is very difficult to help you.
>>> It could be that your smearing parameter is too large.
>>>
>>>
>>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <
>>> sumanchowdhur...@gmail.com>:
>>>
 Dear SIESTA User,

 Recently I am getting some confusing results by using SIESTA. While
 plotting a band structure I am getting a band gap which is quite large.
 However, when I am trying to plot its corresponding total partial 
 density
 of states (PDOS), I can clearly see that there is no existence of any 
 band
 gap. But interestingly the component PDOS are giving the required band 
 gap.
 The problem is with the total PDOS. Do any of you have any idea about 
 these
 kinds of results...

 --
 *Dr. Suman Chowdhury*



 *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
 79, West Bengal, India.*


>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>> 79, West Bengal, India.*
>>
>>
>>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
> 79, West Bengal, India.*
> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>
>


 --
 Kind regards Nick

>>>
>>>
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Just let me know how did you calculate the DOS..

On Sat, Feb 3, 2018 at 3:04 AM, Nick Papior  wrote:

> Dear Suman,
>
> I think you should solve this yourself.
>
> 2018-02-02 5:56 GMT+01:00 Suman Chowdhury :
>
>> Dear Nick Papior,
>>
>> Thank you so so much for your help. Can you help me in this regard about
>> how I can get the correct coordinates for plotting the band structure??
>>
>> On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior  wrote:
>>
>>> If I run your system without performing cell relaxations I find the
>>> attached eigenvalues (for the Monkhorst-Pack grid).
>>>
>>> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
>>> cell-relaxation does not change the spectrum drastically then this is what
>>> you should suspect in the PDOS.
>>> Secondly, the PDOS is *exactly* reproducing the bandgab in this
>>> calculation.
>>>
>>> 1) I would highly suggest you to perform cell/coordinate relaxations in
>>> one directory, then afterwards perform analysis on the relaxed structure,
>>> PDOS, band-structure, optical, etc.
>>> 2) Possibly your band-structure coordinates are wrong because when I
>>> plot the bandstructure for this structure it does not capture the correct
>>> band gab (this *has* to be the problem).
>>>
>>> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury :
>>>
 I have just tried to see the variation of TDOS by changing the smearing
 parameter. But I could not observe any change in it.

 On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
 sumanchowdhur...@gmail.com> wrote:

> This is the fdf that I have used...
>
> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
> wrote:
>
>> Dear Suman,
>>
>> Without data (plots) or fdf file it is very difficult to help you.
>> It could be that your smearing parameter is too large.
>>
>>
>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <
>> sumanchowdhur...@gmail.com>:
>>
>>> Dear SIESTA User,
>>>
>>> Recently I am getting some confusing results by using SIESTA. While
>>> plotting a band structure I am getting a band gap which is quite large.
>>> However, when I am trying to plot its corresponding total partial 
>>> density
>>> of states (PDOS), I can clearly see that there is no existence of any 
>>> band
>>> gap. But interestingly the component PDOS are giving the required band 
>>> gap.
>>> The problem is with the total PDOS. Do any of you have any idea about 
>>> these
>>> kinds of results...
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
> 79, West Bengal, India.*
>
>
>


 --
 *Dr. Suman Chowdhury*



 *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232 <+91%2098305%2012232>*


>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Nick Papior]

Dear Suman,

I think you should solve this yourself.

2018-02-02 5:56 GMT+01:00 Suman Chowdhury :

> Dear Nick Papior,
>
> Thank you so so much for your help. Can you help me in this regard about
> how I can get the correct coordinates for plotting the band structure??
>
> On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior  wrote:
>
>> If I run your system without performing cell relaxations I find the
>> attached eigenvalues (for the Monkhorst-Pack grid).
>>
>> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
>> cell-relaxation does not change the spectrum drastically then this is what
>> you should suspect in the PDOS.
>> Secondly, the PDOS is *exactly* reproducing the bandgab in this
>> calculation.
>>
>> 1) I would highly suggest you to perform cell/coordinate relaxations in
>> one directory, then afterwards perform analysis on the relaxed structure,
>> PDOS, band-structure, optical, etc.
>> 2) Possibly your band-structure coordinates are wrong because when I plot
>> the bandstructure for this structure it does not capture the correct band
>> gab (this *has* to be the problem).
>>
>> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury :
>>
>>> I have just tried to see the variation of TDOS by changing the smearing
>>> parameter. But I could not observe any change in it.
>>>
>>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>>> sumanchowdhur...@gmail.com> wrote:
>>>
 This is the fdf that I have used...

 On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
 wrote:

> Dear Suman,
>
> Without data (plots) or fdf file it is very difficult to help you.
> It could be that your smearing parameter is too large.
>
>
> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury  >:
>
>> Dear SIESTA User,
>>
>> Recently I am getting some confusing results by using SIESTA. While
>> plotting a band structure I am getting a band gap which is quite large.
>> However, when I am trying to plot its corresponding total partial density
>> of states (PDOS), I can clearly see that there is no existence of any 
>> band
>> gap. But interestingly the component PDOS are giving the required band 
>> gap.
>> The problem is with the total PDOS. Do any of you have any idea about 
>> these
>> kinds of results...
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>> 79, West Bengal, India.*
>>
>>
>
>
> --
> Kind regards Nick
>



 --
 *Dr. Suman Chowdhury*



 *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
 79, West Bengal, India.*



>>>
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Dear Nick Papior,

Thank you so so much for your help. Can you help me in this regard about
how I can get the correct coordinates for plotting the band structure??

On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior  wrote:

> If I run your system without performing cell relaxations I find the
> attached eigenvalues (for the Monkhorst-Pack grid).
>
> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
> cell-relaxation does not change the spectrum drastically then this is what
> you should suspect in the PDOS.
> Secondly, the PDOS is *exactly* reproducing the bandgab in this
> calculation.
>
> 1) I would highly suggest you to perform cell/coordinate relaxations in
> one directory, then afterwards perform analysis on the relaxed structure,
> PDOS, band-structure, optical, etc.
> 2) Possibly your band-structure coordinates are wrong because when I plot
> the bandstructure for this structure it does not capture the correct band
> gab (this *has* to be the problem).
>
> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury :
>
>> I have just tried to see the variation of TDOS by changing the smearing
>> parameter. But I could not observe any change in it.
>>
>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>> sumanchowdhur...@gmail.com> wrote:
>>
>>> This is the fdf that I have used...
>>>
>>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
>>> wrote:
>>>
 Dear Suman,

 Without data (plots) or fdf file it is very difficult to help you.
 It could be that your smearing parameter is too large.


 2018-01-24 15:13 GMT+01:00 Suman Chowdhury 
 :

> Dear SIESTA User,
>
> Recently I am getting some confusing results by using SIESTA. While
> plotting a band structure I am getting a band gap which is quite large.
> However, when I am trying to plot its corresponding total partial density
> of states (PDOS), I can clearly see that there is no existence of any band
> gap. But interestingly the component PDOS are giving the required band 
> gap.
> The problem is with the total PDOS. Do any of you have any idea about 
> these
> kinds of results...
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
> 79, West Bengal, India.*
>
>


 --
 Kind regards Nick

>>>
>>>
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>>
>>>
>>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Nick Papior]

If I run your system without performing cell relaxations I find the
attached eigenvalues (for the Monkhorst-Pack grid).

In this case there is *only* a bandgab of ~0.5 eV. Provided that the
cell-relaxation does not change the spectrum drastically then this is what
you should suspect in the PDOS.
Secondly, the PDOS is *exactly* reproducing the bandgab in this calculation.

1) I would highly suggest you to perform cell/coordinate relaxations in one
directory, then afterwards perform analysis on the relaxed structure, PDOS,
band-structure, optical, etc.
2) Possibly your band-structure coordinates are wrong because when I plot
the bandstructure for this structure it does not capture the correct band
gab (this *has* to be the problem).

2018-01-31 16:35 GMT+01:00 Suman Chowdhury :

> I have just tried to see the variation of TDOS by changing the smearing
> parameter. But I could not observe any change in it.
>
> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
> sumanchowdhur...@gmail.com> wrote:
>
>> This is the fdf that I have used...
>>
>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
>> wrote:
>>
>>> Dear Suman,
>>>
>>> Without data (plots) or fdf file it is very difficult to help you.
>>> It could be that your smearing parameter is too large.
>>>
>>>
>>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury :
>>>
 Dear SIESTA User,

 Recently I am getting some confusing results by using SIESTA. While
 plotting a band structure I am getting a band gap which is quite large.
 However, when I am trying to plot its corresponding total partial density
 of states (PDOS), I can clearly see that there is no existence of any band
 gap. But interestingly the component PDOS are giving the required band gap.
 The problem is with the total PDOS. Do any of you have any idea about these
 kinds of results...

 --
 *Dr. Suman Chowdhury*



 *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
 79, West Bengal, India.*


>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>>
>>
>>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

I have just tried to see the variation of TDOS by changing the smearing
parameter. But I could not observe any change in it.

On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury  wrote:

> This is the fdf that I have used...
>
> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior 
> wrote:
>
>> Dear Suman,
>>
>> Without data (plots) or fdf file it is very difficult to help you.
>> It could be that your smearing parameter is too large.
>>
>>
>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury :
>>
>>> Dear SIESTA User,
>>>
>>> Recently I am getting some confusing results by using SIESTA. While
>>> plotting a band structure I am getting a band gap which is quite large.
>>> However, when I am trying to plot its corresponding total partial density
>>> of states (PDOS), I can clearly see that there is no existence of any band
>>> gap. But interestingly the component PDOS are giving the required band gap.
>>> The problem is with the total PDOS. Do any of you have any idea about these
>>> kinds of results...
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
>
>
>


-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

This is the fdf that I have used...

On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior  wrote:

> Dear Suman,
>
> Without data (plots) or fdf file it is very difficult to help you.
> It could be that your smearing parameter is too large.
>
>
> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury :
>
>> Dear SIESTA User,
>>
>> Recently I am getting some confusing results by using SIESTA. While
>> plotting a band structure I am getting a band gap which is quite large.
>> However, when I am trying to plot its corresponding total partial density
>> of states (PDOS), I can clearly see that there is no existence of any band
>> gap. But interestingly the component PDOS are giving the required band gap.
>> The problem is with the total PDOS. Do any of you have any idea about these
>> kinds of results...
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*


SiC.fdf
Description: Binary data

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Nick Papior]

Dear Suman,

Without data (plots) or fdf file it is very difficult to help you.
It could be that your smearing parameter is too large.


2018-01-24 15:13 GMT+01:00 Suman Chowdhury :

> Dear SIESTA User,
>
> Recently I am getting some confusing results by using SIESTA. While
> plotting a band structure I am getting a band gap which is quite large.
> However, when I am trying to plot its corresponding total partial density
> of states (PDOS), I can clearly see that there is no existence of any band
> gap. But interestingly the component PDOS are giving the required band gap.
> The problem is with the total PDOS. Do any of you have any idea about these
> kinds of results...
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Band Structure and PDOS results not matching

[sauluck]

For energy gap look at TDOS not PDOS


> Dear SIESTA User,
>
> Recently I am getting some confusing results by using SIESTA. While
> plotting a band structure I am getting a band gap which is quite large.
> However, when I am trying to plot its corresponding total partial density
> of states (PDOS), I can clearly see that there is no existence of any band
> gap. But interestingly the component PDOS are giving the required band
> gap.
> The problem is with the total PDOS. Do any of you have any idea about
> these
> kinds of results...
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
> * Ph no-+91-9830512232*
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
http://www.nplindia.org/prof-sushil-auluck
http://www.iitk.ac.in/phy/index.php/component/content/article/2-uncategorised/124-sushil-auluck
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
http://www.iitk.ac.in/phy/index.php/people/faculty
http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
...
~

[SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Dear SIESTA User,

Recently I am getting some confusing results by using SIESTA. While
plotting a band structure I am getting a band gap which is quite large.
However, when I am trying to plot its corresponding total partial density
of states (PDOS), I can clearly see that there is no existence of any band
gap. But interestingly the component PDOS are giving the required band gap.
The problem is with the total PDOS. Do any of you have any idea about these
kinds of results...

-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] band structure

[I. Camps]

The first thing you have to know is not how SIESTA calculate certain
property.

The firs thing you have to know is the physical meaning of the property.
Then ask about how SIESTA calculate it, or better, read the manual first,
search the SIESTA mail list and then ask.

Read/search for the following:
- Solid State Physics
- Semiconductor Physics
- Inverse or reciprocal space
- Brillouin zone (this will answer your question about "the matrix numbers")



[]'s,

Camps

On Wed, Aug 10, 2016 at 5:02 AM, amrish sharma  wrote:

> %block BandLines
> 1 1.000 1.000 1.000 L # Begin at L
> 20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
> 25 2.000 0.000 0.000 X # 25 points from gamma to X
> 30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
> %endblock BandLines
>
>
> WHAT DOES THIS MATRIX TYPE NUMBERS REPRESENT
> EX. 1.0 1.0 1.0 LIKE IN L ETC.
>
> On Wed, Aug 10, 2016 at 12:53 PM, Nick Papior 
> wrote:
>
>> Please read the manual from page 71.
>>
>> Note this is the manual 4.0 located here:
>> https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf
>>
>> 2016-08-10 8:35 GMT+02:00 amrish sharma :
>>
>>> hii all user
>>>
>>> i want to know how to get band structure plot in siesta ?
>>>
>>> --
>>> warm regards
>>>
>>> amrish sharma
>>>
>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> warm regards
>
> amrish sharma
>

Re: [SIESTA-L] band structure

[amrish sharma]

%block BandLines
1 1.000 1.000 1.000 L # Begin at L
20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
25 2.000 0.000 0.000 X # 25 points from gamma to X
30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
%endblock BandLines


WHAT DOES THIS MATRIX TYPE NUMBERS REPRESENT
EX. 1.0 1.0 1.0 LIKE IN L ETC.

On Wed, Aug 10, 2016 at 12:53 PM, Nick Papior  wrote:

> Please read the manual from page 71.
>
> Note this is the manual 4.0 located here:
> https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf
>
> 2016-08-10 8:35 GMT+02:00 amrish sharma :
>
>> hii all user
>>
>> i want to know how to get band structure plot in siesta ?
>>
>> --
>> warm regards
>>
>> amrish sharma
>>
>
>
>
> --
> Kind regards Nick
>



-- 
warm regards

amrish sharma

Re: [SIESTA-L] band structure

[Nick Papior]

Please read the manual from page 71.

Note this is the manual 4.0 located here:
https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf

2016-08-10 8:35 GMT+02:00 amrish sharma :

> hii all user
>
> i want to know how to get band structure plot in siesta ?
>
> --
> warm regards
>
> amrish sharma
>



-- 
Kind regards Nick

[SIESTA-L] band structure

[amrish sharma]

hii all user

i want to know how to get band structure plot in siesta ?

-- 
warm regards

amrish sharma

Re: [SIESTA-L] Band structure for doped ZGNR

[maryam jamaati]

Hi,

Yes I have a supercell instead of one unit cell of ZGNR.

BW,


On Sun, Jul 31, 2016 at 1:19 AM, Максим Арсентьев 
wrote:

> so you mean because of doping you have a supercell now? Anyway your system
> still have symmmetry - for choosing k - points use this paper. It is
>  general manner. I did not dealt with supercells but do not think your
> problem is critical.
>
> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>
>> Doped means is it replacement of carbon or other molecule in vicinity?
>>
>> On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:
>>
>>> Dear siesta users,
>>>
>>> According to helpful advices of some friends (Nick, Kamaraj,..), I
>>> reduced geometry to unit cell for calculation of ZGNR band structure.
>>> Whether we have to use minimal unit cell for doped ZGNR or not?
>>>
>>> Kind regards,
>>>
>>> Maryam Jamaati
>>>
>>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>

Re: [SIESTA-L] Band structure for doped ZGNR

[I. Camps]

Hi Riya,

You can do your own program and generate all the possible structures. Today
computers with fast multiprocessors (and graphical cards), lot of Hds space
and RAM memory are able to accomplish this task. (Using fragment based drug
design I already worked with 5.5 million of structures in a 8-core with 2TB
of HD and 16GM of RAM).

What about "after" all the structures are generated? Will you do ab initio
calculations with all of them? I don't think so.
One way to overcome this is to select the "best" structure. To select the
"best" of anything you must use a criterion. In this case, the entropy of
the system is used. The program ATAT makes use of Monte Carlo to generate
it.
The other program (USPEX) is specialized in predicting new crystal
structures using semi-empirical and ab initio codes using as criterion
other properties (entropy, heat of formation, hardness, etc.)


[]'s,

Camps

On Sun, Jul 31, 2016 at 9:59 AM, Riya Rogers 
wrote:

> Ok so tht means tht checking each config is nt possible but if possible
> its a valid method
>
> On 31-Jul-2016 6:16 pm, "I. Camps"  wrote:
>
>> Take a look here:
>>
>> http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
>>
>> If you will test all the possible combinations, you will do a massive
>> work.
>>
>> For example, if you have 100 Atmos, and a dropping concentration of 5%
>> (replace 5 atoms), you have to explore all the combination: 7.5E7.
>>
>> With the quase random structures theory, you get the best (must
>> representative) structure.
>>
>> On Sun, Jul 31, 2016, 08:54 Максим Арсентьев 
>> wrote:
>>
>>> Hi, Camps,
>>> What do you mean "is generated based in disorder and entropy" pls. give
>>> a link. As i know till now to find a place for dopant you should to try all
>>> possible combinations and the combination with the lowes energy is correct.
>>> This i know other researchers do, but your route is unknown for me, explain.
>>>
>>> 2016-07-31 13:30 GMT+04:00 Riya Rogers :
>>>
 Primitive means smallest cell possible so it contains few atoms so your
 doping percentage is higher

 On 31-Jul-2016 6:16 am, "I. Camps"  wrote:

> Hello,
>
> If you use doping, you can not (or should not) use the primitive cell.
> This is because you will need to select a % of atoms to substitute that
> aren't enough in the primitive (or minimal) cell, so you have to use a
> bigger cell (supercell) with greater number of atoms. Using the primitive
> cell, will generate a crystal not dopped. A dopped crystal has a "few"
> extra or substituted atoms.
>
> Other problem is how will you select the corresponding atom (or site)
> for substitution. You have to use a theory to help you with this task. One
> of them is the use of quase random structures where the "best" structure 
> is
> generated based in disorder and entropy.
>
> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
> wrote:
>
>> so you mean because of doping you have a supercell now? Anyway your
>> system still have symmmetry - for choosing k - points use this paper. It 
>> is
>>  general manner. I did not dealt with supercells but do not think your
>> problem is critical.
>>
>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>
>>> Doped means is it replacement of carbon or other molecule in
>>> vicinity?
>>>
>>> On 30-Jul-2016 10:38 pm, "maryam jamaati" 
>>> wrote:
>>>
 Dear siesta users,

 According to helpful advices of some friends (Nick, Kamaraj,..), I
 reduced geometry to unit cell for calculation of ZGNR band structure.
 Whether we have to use minimal unit cell for doped ZGNR or not?

 Kind regards,

 Maryam Jamaati


>>
>>
>> --
>> Best wishes,
>> Maxim Arsent'ev, Ph.D. (Chemistry)
>> Laboratory of research of nanostructures
>> Institute of Silicate Chemistry of RAS
>>
> --
>
> []`s
>
> Camps
>

>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>

Re: [SIESTA-L] Band structure for doped ZGNR

[I. Camps]

Hi Riya and Маxim,

In this link you can find a paper about Special Quasirandom Structures
theory (
https://www.researchgate.net/publication/13246916_Special_Quasirandom_Structures),
also, a Google link (
https://www.google.com.br/search?q=%22Special+Quasirandom+Structure%22=utf-8=utf-8=firefox-b_rd=cr=Fo-eV6dS86nzB6TSqogL
).

This theory is used to study alloys and extended to doped/vacancies in
crystals.

The ATAT program is able, starting from a given primitive cell and
specifying the final number of atoms of the supercell and the % of atom
substitution/vacancies, to generate the best supercell with the given
doping  concentration.
(This software do many other interesting things!)

Other program that is able to generate special qausirandom structures is
USPEX (http://uspex.stonybrook.edu/)

Both programs generate new structures.

[]'s,

Camps




On Sun, Jul 31, 2016 at 6:07 PM, Максим Арсентьев 
wrote:

> Hi, Camps,
> So ATAT randomly places atoms and approximates? Does it able to create new
> structures, or only places atoms to positions (i believe it is not)?
>
> 2016-07-31 16:59 GMT+04:00 Riya Rogers :
>
>> Ok so tht means tht checking each config is nt possible but if possible
>> its a valid method
>>
>> On 31-Jul-2016 6:16 pm, "I. Camps"  wrote:
>>
>>> Take a look here:
>>>
>>> http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
>>>
>>> If you will test all the possible combinations, you will do a massive
>>> work.
>>>
>>> For example, if you have 100 Atmos, and a dropping concentration of 5%
>>> (replace 5 atoms), you have to explore all the combination: 7.5E7.
>>>
>>> With the quase random structures theory, you get the best (must
>>> representative) structure.
>>>
>>> On Sun, Jul 31, 2016, 08:54 Максим Арсентьев 
>>> wrote:
>>>
 Hi, Camps,
 What do you mean "is generated based in disorder and entropy" pls.
 give a link. As i know till now to find a place for dopant you should to
 try all possible combinations and the combination with the lowes energy is
 correct. This i know other researchers do, but your route is unknown for
 me, explain.

 2016-07-31 13:30 GMT+04:00 Riya Rogers :

> Primitive means smallest cell possible so it contains few atoms so
> your doping percentage is higher
>
> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>
>> Hello,
>>
>> If you use doping, you can not (or should not) use the primitive
>> cell. This is because you will need to select a % of atoms to substitute
>> that aren't enough in the primitive (or minimal) cell, so you have to 
>> use a
>> bigger cell (supercell) with greater number of atoms. Using the primitive
>> cell, will generate a crystal not dopped. A dopped crystal has a "few"
>> extra or substituted atoms.
>>
>> Other problem is how will you select the corresponding atom (or site)
>> for substitution. You have to use a theory to help you with this task. 
>> One
>> of them is the use of quase random structures where the "best" structure 
>> is
>> generated based in disorder and entropy.
>>
>> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
>> wrote:
>>
>>> so you mean because of doping you have a supercell now? Anyway your
>>> system still have symmmetry - for choosing k - points use this paper. 
>>> It is
>>>  general manner. I did not dealt with supercells but do not think your
>>> problem is critical.
>>>
>>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>>
 Doped means is it replacement of carbon or other molecule in
 vicinity?

 On 30-Jul-2016 10:38 pm, "maryam jamaati" 
 wrote:

> Dear siesta users,
>
> According to helpful advices of some friends (Nick, Kamaraj,..), I
> reduced geometry to unit cell for calculation of ZGNR band structure.
> Whether we have to use minimal unit cell for doped ZGNR or not?
>
> Kind regards,
>
> Maryam Jamaati
>
>
>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>


 --
 Best wishes,
 Maxim Arsent'ev, Ph.D. (Chemistry)
 Laboratory of research of nanostructures
 Institute of Silicate Chemistry of RAS

>>> --
>>>
>>> []`s
>>>
>>> Camps
>>>
>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>

Re: [SIESTA-L] Band structure for doped ZGNR

[Максим Арсентьев]

Hi, Camps,
So ATAT randomly places atoms and approximates? Does it able to create new
structures, or only places atoms to positions (i believe it is not)?

2016-07-31 16:59 GMT+04:00 Riya Rogers :

> Ok so tht means tht checking each config is nt possible but if possible
> its a valid method
>
> On 31-Jul-2016 6:16 pm, "I. Camps"  wrote:
>
>> Take a look here:
>>
>> http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
>>
>> If you will test all the possible combinations, you will do a massive
>> work.
>>
>> For example, if you have 100 Atmos, and a dropping concentration of 5%
>> (replace 5 atoms), you have to explore all the combination: 7.5E7.
>>
>> With the quase random structures theory, you get the best (must
>> representative) structure.
>>
>> On Sun, Jul 31, 2016, 08:54 Максим Арсентьев 
>> wrote:
>>
>>> Hi, Camps,
>>> What do you mean "is generated based in disorder and entropy" pls. give
>>> a link. As i know till now to find a place for dopant you should to try all
>>> possible combinations and the combination with the lowes energy is correct.
>>> This i know other researchers do, but your route is unknown for me, explain.
>>>
>>> 2016-07-31 13:30 GMT+04:00 Riya Rogers :
>>>
 Primitive means smallest cell possible so it contains few atoms so your
 doping percentage is higher

 On 31-Jul-2016 6:16 am, "I. Camps"  wrote:

> Hello,
>
> If you use doping, you can not (or should not) use the primitive cell.
> This is because you will need to select a % of atoms to substitute that
> aren't enough in the primitive (or minimal) cell, so you have to use a
> bigger cell (supercell) with greater number of atoms. Using the primitive
> cell, will generate a crystal not dopped. A dopped crystal has a "few"
> extra or substituted atoms.
>
> Other problem is how will you select the corresponding atom (or site)
> for substitution. You have to use a theory to help you with this task. One
> of them is the use of quase random structures where the "best" structure 
> is
> generated based in disorder and entropy.
>
> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
> wrote:
>
>> so you mean because of doping you have a supercell now? Anyway your
>> system still have symmmetry - for choosing k - points use this paper. It 
>> is
>>  general manner. I did not dealt with supercells but do not think your
>> problem is critical.
>>
>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>
>>> Doped means is it replacement of carbon or other molecule in
>>> vicinity?
>>>
>>> On 30-Jul-2016 10:38 pm, "maryam jamaati" 
>>> wrote:
>>>
 Dear siesta users,

 According to helpful advices of some friends (Nick, Kamaraj,..), I
 reduced geometry to unit cell for calculation of ZGNR band structure.
 Whether we have to use minimal unit cell for doped ZGNR or not?

 Kind regards,

 Maryam Jamaati


>>
>>
>> --
>> Best wishes,
>> Maxim Arsent'ev, Ph.D. (Chemistry)
>> Laboratory of research of nanostructures
>> Institute of Silicate Chemistry of RAS
>>
> --
>
> []`s
>
> Camps
>

>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>


-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS

Re: [SIESTA-L] Band structure for doped ZGNR

[Riya Rogers]

Ok so tht means tht checking each config is nt possible but if possible its
a valid method

On 31-Jul-2016 6:16 pm, "I. Camps"  wrote:

> Take a look here:
>
> http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
>
> If you will test all the possible combinations, you will do a massive work.
>
> For example, if you have 100 Atmos, and a dropping concentration of 5%
> (replace 5 atoms), you have to explore all the combination: 7.5E7.
>
> With the quase random structures theory, you get the best (must
> representative) structure.
>
> On Sun, Jul 31, 2016, 08:54 Максим Арсентьев 
> wrote:
>
>> Hi, Camps,
>> What do you mean "is generated based in disorder and entropy" pls. give
>> a link. As i know till now to find a place for dopant you should to try all
>> possible combinations and the combination with the lowes energy is correct.
>> This i know other researchers do, but your route is unknown for me, explain.
>>
>> 2016-07-31 13:30 GMT+04:00 Riya Rogers :
>>
>>> Primitive means smallest cell possible so it contains few atoms so your
>>> doping percentage is higher
>>>
>>> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>>>
 Hello,

 If you use doping, you can not (or should not) use the primitive cell.
 This is because you will need to select a % of atoms to substitute that
 aren't enough in the primitive (or minimal) cell, so you have to use a
 bigger cell (supercell) with greater number of atoms. Using the primitive
 cell, will generate a crystal not dopped. A dopped crystal has a "few"
 extra or substituted atoms.

 Other problem is how will you select the corresponding atom (or site)
 for substitution. You have to use a theory to help you with this task. One
 of them is the use of quase random structures where the "best" structure is
 generated based in disorder and entropy.

 On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
 wrote:

> so you mean because of doping you have a supercell now? Anyway your
> system still have symmmetry - for choosing k - points use this paper. It 
> is
>  general manner. I did not dealt with supercells but do not think your
> problem is critical.
>
> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>
>> Doped means is it replacement of carbon or other molecule in vicinity?
>>
>> On 30-Jul-2016 10:38 pm, "maryam jamaati" 
>> wrote:
>>
>>> Dear siesta users,
>>>
>>> According to helpful advices of some friends (Nick, Kamaraj,..), I
>>> reduced geometry to unit cell for calculation of ZGNR band structure.
>>> Whether we have to use minimal unit cell for doped ZGNR or not?
>>>
>>> Kind regards,
>>>
>>> Maryam Jamaati
>>>
>>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>
 --

 []`s

 Camps

>>>
>>
>>
>> --
>> Best wishes,
>> Maxim Arsent'ev, Ph.D. (Chemistry)
>> Laboratory of research of nanostructures
>> Institute of Silicate Chemistry of RAS
>>
> --
>
> []`s
>
> Camps
>

Re: [SIESTA-L] Band structure for doped ZGNR

[I. Camps]

Take a look here:

http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/

If you will test all the possible combinations, you will do a massive work.

For example, if you have 100 Atmos, and a dropping concentration of 5%
(replace 5 atoms), you have to explore all the combination: 7.5E7.

With the quase random structures theory, you get the best (must
representative) structure.

On Sun, Jul 31, 2016, 08:54 Максим Арсентьев  wrote:

> Hi, Camps,
> What do you mean "is generated based in disorder and entropy" pls. give a
> link. As i know till now to find a place for dopant you should to try all
> possible combinations and the combination with the lowes energy is correct.
> This i know other researchers do, but your route is unknown for me, explain.
>
> 2016-07-31 13:30 GMT+04:00 Riya Rogers :
>
>> Primitive means smallest cell possible so it contains few atoms so your
>> doping percentage is higher
>>
>> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>>
>>> Hello,
>>>
>>> If you use doping, you can not (or should not) use the primitive cell.
>>> This is because you will need to select a % of atoms to substitute that
>>> aren't enough in the primitive (or minimal) cell, so you have to use a
>>> bigger cell (supercell) with greater number of atoms. Using the primitive
>>> cell, will generate a crystal not dopped. A dopped crystal has a "few"
>>> extra or substituted atoms.
>>>
>>> Other problem is how will you select the corresponding atom (or site)
>>> for substitution. You have to use a theory to help you with this task. One
>>> of them is the use of quase random structures where the "best" structure is
>>> generated based in disorder and entropy.
>>>
>>> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
>>> wrote:
>>>
 so you mean because of doping you have a supercell now? Anyway your
 system still have symmmetry - for choosing k - points use this paper. It is
  general manner. I did not dealt with supercells but do not think your
 problem is critical.

 2016-07-30 23:00 GMT+04:00 Riya Rogers :

> Doped means is it replacement of carbon or other molecule in vicinity?
>
> On 30-Jul-2016 10:38 pm, "maryam jamaati" 
> wrote:
>
>> Dear siesta users,
>>
>> According to helpful advices of some friends (Nick, Kamaraj,..), I
>> reduced geometry to unit cell for calculation of ZGNR band structure.
>> Whether we have to use minimal unit cell for doped ZGNR or not?
>>
>> Kind regards,
>>
>> Maryam Jamaati
>>
>>


 --
 Best wishes,
 Maxim Arsent'ev, Ph.D. (Chemistry)
 Laboratory of research of nanostructures
 Institute of Silicate Chemistry of RAS

>>> --
>>>
>>> []`s
>>>
>>> Camps
>>>
>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>
-- 

[]`s

Camps

Re: [SIESTA-L] Band structure for doped ZGNR

[RAJAN SINGH]

Even according to me you should to try all possible combinations and the
combination with the lowes energy is correct.

This is wht is done by researchers.
In dft it is assumed tht everything is done at close to absolute temp. So
entropy is very less.

On 31-Jul-2016 5:25 pm, "Максим Арсентьев"  wrote:

Hi, Camps,
What do you mean "is generated based in disorder and entropy" pls. give a
link. As i know till now to find a place for dopant you should to try all
possible combinations and the combination with the lowes energy is correct.
This i know other researchers do, but your route is unknown for me, explain.

2016-07-31 13:30 GMT+04:00 Riya Rogers :

> Primitive means smallest cell possible so it contains few atoms so your
> doping percentage is higher
>
> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>
>> Hello,
>>
>> If you use doping, you can not (or should not) use the primitive cell.
>> This is because you will need to select a % of atoms to substitute that
>> aren't enough in the primitive (or minimal) cell, so you have to use a
>> bigger cell (supercell) with greater number of atoms. Using the primitive
>> cell, will generate a crystal not dopped. A dopped crystal has a "few"
>> extra or substituted atoms.
>>
>> Other problem is how will you select the corresponding atom (or site) for
>> substitution. You have to use a theory to help you with this task. One of
>> them is the use of quase random structures where the "best" structure is
>> generated based in disorder and entropy.
>>
>> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
>> wrote:
>>
>>> so you mean because of doping you have a supercell now? Anyway your
>>> system still have symmmetry - for choosing k - points use this paper. It is
>>>  general manner. I did not dealt with supercells but do not think your
>>> problem is critical.
>>>
>>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>>
 Doped means is it replacement of carbon or other molecule in vicinity?

 On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:

> Dear siesta users,
>
> According to helpful advices of some friends (Nick, Kamaraj,..), I
> reduced geometry to unit cell for calculation of ZGNR band structure.
> Whether we have to use minimal unit cell for doped ZGNR or not?
>
> Kind regards,
>
> Maryam Jamaati
>
>
>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>


-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS

Re: [SIESTA-L] Band structure for doped ZGNR

[Максим Арсентьев]

Hi, Camps,
What do you mean "is generated based in disorder and entropy" pls. give a
link. As i know till now to find a place for dopant you should to try all
possible combinations and the combination with the lowes energy is correct.
This i know other researchers do, but your route is unknown for me, explain.

2016-07-31 13:30 GMT+04:00 Riya Rogers :

> Primitive means smallest cell possible so it contains few atoms so your
> doping percentage is higher
>
> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>
>> Hello,
>>
>> If you use doping, you can not (or should not) use the primitive cell.
>> This is because you will need to select a % of atoms to substitute that
>> aren't enough in the primitive (or minimal) cell, so you have to use a
>> bigger cell (supercell) with greater number of atoms. Using the primitive
>> cell, will generate a crystal not dopped. A dopped crystal has a "few"
>> extra or substituted atoms.
>>
>> Other problem is how will you select the corresponding atom (or site) for
>> substitution. You have to use a theory to help you with this task. One of
>> them is the use of quase random structures where the "best" structure is
>> generated based in disorder and entropy.
>>
>> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
>> wrote:
>>
>>> so you mean because of doping you have a supercell now? Anyway your
>>> system still have symmmetry - for choosing k - points use this paper. It is
>>>  general manner. I did not dealt with supercells but do not think your
>>> problem is critical.
>>>
>>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>>
 Doped means is it replacement of carbon or other molecule in vicinity?

 On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:

> Dear siesta users,
>
> According to helpful advices of some friends (Nick, Kamaraj,..), I
> reduced geometry to unit cell for calculation of ZGNR band structure.
> Whether we have to use minimal unit cell for doped ZGNR or not?
>
> Kind regards,
>
> Maryam Jamaati
>
>
>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>


-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS

Re: [SIESTA-L] Band structure for doped ZGNR

[Riya Rogers]

Primitive means smallest cell possible so it contains few atoms so your
doping percentage is higher

On 31-Jul-2016 6:16 am, "I. Camps"  wrote:

> Hello,
>
> If you use doping, you can not (or should not) use the primitive cell.
> This is because you will need to select a % of atoms to substitute that
> aren't enough in the primitive (or minimal) cell, so you have to use a
> bigger cell (supercell) with greater number of atoms. Using the primitive
> cell, will generate a crystal not dopped. A dopped crystal has a "few"
> extra or substituted atoms.
>
> Other problem is how will you select the corresponding atom (or site) for
> substitution. You have to use a theory to help you with this task. One of
> them is the use of quase random structures where the "best" structure is
> generated based in disorder and entropy.
>
> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
> wrote:
>
>> so you mean because of doping you have a supercell now? Anyway your
>> system still have symmmetry - for choosing k - points use this paper. It is
>>  general manner. I did not dealt with supercells but do not think your
>> problem is critical.
>>
>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>
>>> Doped means is it replacement of carbon or other molecule in vicinity?
>>>
>>> On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:
>>>
 Dear siesta users,

 According to helpful advices of some friends (Nick, Kamaraj,..), I
 reduced geometry to unit cell for calculation of ZGNR band structure.
 Whether we have to use minimal unit cell for doped ZGNR or not?

 Kind regards,

 Maryam Jamaati


>>
>>
>> --
>> Best wishes,
>> Maxim Arsent'ev, Ph.D. (Chemistry)
>> Laboratory of research of nanostructures
>> Institute of Silicate Chemistry of RAS
>>
> --
>
> []`s
>
> Camps
>

Re: [SIESTA-L] Band structure for doped ZGNR

[I. Camps]

Hello,

If you use doping, you can not (or should not) use the primitive cell. This
is because you will need to select a % of atoms to substitute that aren't
enough in the primitive (or minimal) cell, so you have to use a bigger cell
(supercell) with greater number of atoms. Using the primitive cell, will
generate a crystal not dopped. A dopped crystal has a "few" extra or
substituted atoms.

Other problem is how will you select the corresponding atom (or site) for
substitution. You have to use a theory to help you with this task. One of
them is the use of quase random structures where the "best" structure is
generated based in disorder and entropy.

On Sat, Jul 30, 2016, 17:51 Максим Арсентьев  wrote:

> so you mean because of doping you have a supercell now? Anyway your system
> still have symmmetry - for choosing k - points use this paper. It is
>  general manner. I did not dealt with supercells but do not think your
> problem is critical.
>
> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>
>> Doped means is it replacement of carbon or other molecule in vicinity?
>>
>> On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:
>>
>>> Dear siesta users,
>>>
>>> According to helpful advices of some friends (Nick, Kamaraj,..), I
>>> reduced geometry to unit cell for calculation of ZGNR band structure.
>>> Whether we have to use minimal unit cell for doped ZGNR or not?
>>>
>>> Kind regards,
>>>
>>> Maryam Jamaati
>>>
>>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>
-- 

[]`s

Camps

Re: [SIESTA-L] Band structure for doped ZGNR

[Riya Rogers]

Doped means is it replacement of carbon or other molecule in vicinity?

On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:

> Dear siesta users,
>
> According to helpful advices of some friends (Nick, Kamaraj,..), I reduced
> geometry to unit cell for calculation of ZGNR band structure.
> Whether we have to use minimal unit cell for doped ZGNR or not?
>
> Kind regards,
>
> Maryam Jamaati
>
>

[SIESTA-L] Band structure for doped ZGNR

[maryam jamaati]

Dear siesta users,

According to helpful advices of some friends (Nick, Kamaraj,..), I reduced
geometry to unit cell for calculation of ZGNR band structure.
Whether we have to use minimal unit cell for doped ZGNR or not?

Kind regards,

Maryam Jamaati

Re: [SIESTA-L] Band Structure of ZnS

[Younas Khan]

No, the structures are different. I just want to know whether the lattice
vectors are for the primitive cell of MgO or for conventional cell?

Thanks

On Mon, Jul 27, 2015 at 11:46 AM, fthe...@iesl.forth.gr wrote:

 The lattice vectors in Angstrom are
 5.40930 0 0
 0 5.40930 0
 0 0 5.40930


  Hi all. I am calculating the band structure of ZnS unit cell. I am
  following an exercise for MgO given on SIESTA webpage. The attached Image
  shows the lattice vectors for MgO. Can anybody explain to me in which
  format the lattice vectors are written here? When I do my calculations
 for
  the ZnS, the results look very odd. I am sure that I am writing the
  lattice
  vectors wrong.
 
  [image: Inline image 3]
  (Lattice Vectors for MgO)
 
 
 
  The lattice vectors for ZnS designed in materials studio are:
 
 
  LatticeConstant 5.40930 Ang
  %block LatticeVectors
1.000  0.000  0.000
0.000  1.000  0.000
0.000  0.000  1.000
  %endblock LatticeVectors
 
 
  Thanks
 


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **

Re: [SIESTA-L] Band Structure of ZnS

[sauluck]

hi,
do ZnS ans MgO have the same structure ?
s.auluck

 Hi all. I am calculating the band structure of ZnS unit cell. I am
 following an exercise for MgO given on SIESTA webpage. The attached Image
 shows the lattice vectors for MgO. Can anybody explain to me in which
 format the lattice vectors are written here? When I do my calculations for
 the ZnS, the results look very odd. I am sure that I am writing the
 lattice
 vectors wrong.

 [image: Inline image 3]
 (Lattice Vectors for MgO)



 The lattice vectors for ZnS designed in materials studio are:


 LatticeConstant 5.40930 Ang
 %block LatticeVectors
   1.000  0.000  0.000
   0.000  1.000  0.000
   0.000  0.000  1.000
 %endblock LatticeVectors


 Thanks



-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
http://www.iitk.ac.in/phy/index.php/people/faculty
http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
...
~

Re: [SIESTA-L] Band Structure of ZnS

[fthenak]

The lattice vectors in Angstrom are
5.40930 0 0
0 5.40930 0
0 0 5.40930


 Hi all. I am calculating the band structure of ZnS unit cell. I am
 following an exercise for MgO given on SIESTA webpage. The attached Image
 shows the lattice vectors for MgO. Can anybody explain to me in which
 format the lattice vectors are written here? When I do my calculations for
 the ZnS, the results look very odd. I am sure that I am writing the
 lattice
 vectors wrong.

 [image: Inline image 3]
 (Lattice Vectors for MgO)



 The lattice vectors for ZnS designed in materials studio are:


 LatticeConstant 5.40930 Ang
 %block LatticeVectors
   1.000  0.000  0.000
   0.000  1.000  0.000
   0.000  0.000  1.000
 %endblock LatticeVectors


 Thanks



*
Dr Zacharias G. Fthenakis
Research Associate
Institute of Electronic Structure and Laser (I.E.S.L.)
Foundation for Research and Technology Hellas (FO.R.T.H.)
Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
Phone +30 2810 391824
FAX   +30 2810 391305
webpage: http://esperia.iesl.forth.gr/~fthenak
**

[SIESTA-L] Band Structure of ZnS

[Younas Khan]

Hi all. I am calculating the band structure of ZnS unit cell. I am
following an exercise for MgO given on SIESTA webpage. The attached Image
shows the lattice vectors for MgO. Can anybody explain to me in which
format the lattice vectors are written here? When I do my calculations for
the ZnS, the results look very odd. I am sure that I am writing the lattice
vectors wrong.

[image: Inline image 3]
(Lattice Vectors for MgO)



The lattice vectors for ZnS designed in materials studio are:


LatticeConstant 5.40930 Ang
%block LatticeVectors
  1.000  0.000  0.000
  0.000  1.000  0.000
  0.000  0.000  1.000
%endblock LatticeVectors


Thanks

RE: [SIESTA-L] Band structure of MoSe2

[Salvador Barraza-Lopez]

Dear Xiaoming,

I've read your last e-mail, seen the bands for bulk Mo, and ran out of 
suggestions. Hopefully other members have already worked on the system and can 
provide more detailed input. Your structures look quite symmetric already.



 Best regards,

-Salvador






From: siesta-l-requ...@uam.es siesta-l-requ...@uam.es on behalf of Xiaoming 
Wang xw...@rci.rutgers.edu
Sent: Wednesday, May 6, 2015 2:49 PM
To: siesta-l@uam.es
Subject: RE: [SIESTA-L] Band structure of MoSe2

Dear Salvador,

Thanks so much for your advice and comments! I have compared the band structure 
of bulk Mo from ELK and Siesta with different pseudos (see the attached 
figure). In the figure, CA_07 is the pseudo from 
http://charter.cnf.cornell.edu/psp_files/Mo.psfhttps://urldefense.proofpoint.com/v2/url?u=http-3A__charter.cnf.cornell.edu_psp-5Ffiles_Mo.psfd=AwMFAgc=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQm=8Gk03Ty8ofFbSZtDYEb4s2VF5EJvY-8kxxy1llS4dmks=w_kuCUZlPV9rbDAZtMWyFlmUO_r5Whe6XdxRIpep2Hwe=,
 CA_12 from 
http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/Pseudos_LDA_Abinit/Mo_html/Mo.psfhttps://urldefense.proofpoint.com/v2/url?u=http-3A__departments.icmab.es_leem_siesta_Databases_Pseudopotentials_Pseudos-5FLDA-5FAbinit_Mo-5Fhtml_Mo.psfd=AwMFAgc=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQm=8Gk03Ty8ofFbSZtDYEb4s2VF5EJvY-8kxxy1llS4dmks=l13_3_Z8CMODgL-L1VeJuQNyR9DZXSLG0eUg7C085_ce=,
 and I also tried the pseudo by A. Khein and D.C. Allan as you suggested, the 
result of which is very close to that of CA_12, thus, I don’t show in the Fig.  
As seen from the Fig, I think both of them are acceptable as for bulk band 
structure calculations, but there are some discrepancies about the lattice 
constant. The energy shift of 50 meV was chosen for the calculations, I also 
tried 10 meV of ES, but nearly no significant change can be found. I didn’t 
test the bulk Se calculations, as you have done this.  The relaxed structure is 
attached below which is calculated by using CA_07 of Mo pseudo and Se pseudo 
from Comput. Mater. Sci. , 98 (2015) 372-389,  I think it is 
hexagonal-symmetric, but the K point bands problem still not fixed. And I 
cannot understand how to re-symmetrize the relaxed structure, can you please 
explain a little more? By the way, as you mentioned black phosphorus, I also 
did this kind of calculations before, the problem is not only the gap change 
with some strain as you said but also there are some split about the bands, it 
seems that I turned on the SOC during the calculation. Is this also the result 
of not proper pseudos?

Structure of MoSe2:
  3.248660546   0.0   0.0
 -1.624330273   2.813422563   0.0
  0.0   0.0  13.0
   3
  142   0.4   0.4   0.505632878
  234   0.7   0.2   0.632853521
  234   0.7   0.2   0.378419220


Best regards,

Xiaoming



From: siesta-l-requ...@uam.es [mailto:siesta-l-requ...@uam.es] On Behalf Of 
Salvador Barraza-Lopez
Sent: Friday, May 1, 2015 10:08 AM
To: siesta-l@uam.es
Subject: RE: [SIESTA-L] Band structure of MoSe2


Dear Xiaoming,

Okay, I see. I have some further comments.



You set a relaxation with cell parameters evolving: That setting could be 
responsible for shifting valleys away from the K-point (this similar to the 
effect of K-point shifting induced by strain; this has been discussed 
extensively on other materials with similar structural symmetries and where the 
K-point is special, such as graphene; this is a known effect). So you want to 
re-symmetrize the relaxed structure, especially if the lattice vectors change. 
This may fix the issue near K.



In addition, there is no Mo pseudo on the article you mention, only Se. WSe2 is 
shown as Fig 15 there. Note that there are some discrepancies with VASP results 
on that Figure, and on the bands for W in Figure 10 there as well, but they are 
not nearly as dramatic as the ones you show for MoSe2.



Once your MoSe2 structures are strictly hexagonal-symmetric and fine, may I 
suggest that you compare lattice parameters and band structures for bulk Mo 
with SIESTA and with another code (ELK or Wien2K -all electron codes- could 
work for this purpose). You may want to do the same for Se (we did this for Se 
on the paper you mention, and the datasets are attached as a PDF file here: 
http://www.sciencedirect.com/science/article/pii/S2352340914000353https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sciencedirect.com_science_article_pii_S2352340914000353d=AwMFAgc=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQm=8Gk03Ty8ofFbSZtDYEb4s2VF5EJvY-8kxxy1llS4dmks=Ij4NECQWU-Trdrz4aRYSQCDT_bqt78DrJhnrJkdxwy4e=
 ; we did not work with Mo though

RE: [SIESTA-L] Band structure of MoSe2

[Salvador Barraza-Lopez]

Dear Xiaoming,

Okay, I see. I have some further comments.


You set a relaxation with cell parameters evolving: That setting could be 
responsible for shifting valleys away from the K-point (this similar to the 
effect of K-point shifting induced by strain; this has been discussed 
extensively on other materials with similar structural symmetries and where the 
K-point is special, such as graphene; this is a known effect). So you want to 
re-symmetrize the relaxed structure, especially if the lattice vectors change. 
This may fix the issue near K.


In addition, there is no Mo pseudo on the article you mention, only Se. WSe2 is 
shown as Fig 15 there. Note that there are some discrepancies with VASP results 
on that Figure, and on the bands for W in Figure 10 there as well, but they are 
not nearly as dramatic as the ones you show for MoSe2.


Once your MoSe2 structures are strictly hexagonal-symmetric and fine, may I 
suggest that you compare lattice parameters and band structures for bulk Mo 
with SIESTA and with another code (ELK or Wien2K -all electron codes- could 
work for this purpose). You may want to do the same for Se (we did this for Se 
on the paper you mention, and the datasets are attached as a PDF file here: 
http://www.sciencedirect.com/science/article/pii/S2352340914000353 ; we did not 
work with Mo though).


 Here, you have to recall as well that band structures evolve dramatically with 
strain in 2D materials; so if your lattice constant is 1% off with respect to 
ELK or Wien2K (ie, your optimal parameters are strained as seen from results 
using other codes), you may be seeing gap closings as large as 5% with respect 
to the results of that code as well as other effects in the bands (this is 
another well-known drastic effect of lattice parameters in 2D; this is 
especially seen on black phosphorus).


So to help with Mo, another pseudo you want to try out is the Troullier-Martins 
one generated by A. Khein and D.C. Allan:

http://www.abinit.org/downloads/psp-links/psp-links/lda_tm


For example, the radii in your LDA Mo INP file would have to be:

2.8930462, 3.1973167, and 2.1974630, as found here:

ftp://ftp.abinit.org/pub/abinitio/Psps/LDA_TM.psps/42/42mo.pspnc

That procedure worked for Pt, but you want to see if it does the job for you.


For Mo LDA, these radii currently are 2.75000,  2.89000, and   2.49000, as it 
can be seen on the INP file that you've used at

http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/Pseudos_LDA_Abinit/Mo_html/Mo.html

   pg -- file generated from Mo ps file
tm2
   Mo   ca
 0.000 0.000 0.000 0.000 0.000 0.000
84
50 1.000 0.000#5s
51 0.000 0.000#5p
42 5.000 0.000#4d
43 0.000 0.000#4f
   2.75000   2.89000   2.49000   2.49000   0.0   0.0

#23456789012345678901234567890123456789012345678901234567890  Ruler


you can leave the last channel to be 2.49, that f-channel will not change 
things for you.)



For layered materials, we have also noticed some discrepancies between bulk and 
single-layer results; here is where basis size could also play a role, and 
hence my previous question.


So once again, I would ensure the structure is properly symmetric after 
relaxation, and I would try to reproduce the properties of bulk Mo first, and 
then use that pseudo for MoSe2: There is some additional work ahead for you.


If the symmetries are correct, then you've got to work with the Mo pseudo; 
there will probably be no way around it.


Hopefully this e-mail sets a solid pathway for you to look at. I will be happy 
to learn on your progress.


Best regards,

-Salvador



From: siesta-l-requ...@uam.es siesta-l-requ...@uam.es on behalf of Xiaoming 
Wang xw...@rci.rutgers.edu
Sent: Thursday, April 30, 2015 9:25 PM
To: siesta-l@uam.es
Subject: RE: [SIESTA-L] Band structure of MoSe2

Hi  Salvador,

Thanks for your reply. Changing  the shifts to 0.0 0.0 0.0 actually can’t solve 
the problem. And I have also checked the basis sizes of SZ, SZP, DZ  but not 
beyond DZP,  the ‘non-differential’ point still exists. By the way, I have 
rechecked the band structure, the ‘non-differential’ points can actually also 
be observed at M(0.0, 0.5, 0.0) k-point,  but not as obvious as that of 
K(0.333, 0.333, 0.0) point.
I havn’t tried the bulk band structure yet.

Best regards,

Xiaoming

From: siesta-l-requ...@uam.es [mailto:siesta-l-requ...@uam.es] On Behalf Of 
Salvador Barraza-Lopez
Sent: Thursday, April 30, 2015 9:46 PM
To: siesta-l@uam.es
Subject: RE: [SIESTA-L] Band structure of MoSe2


The only thing that is evident to me at this moment is that you are avoiding 
the K-points in your k-point sampling; as indicated by Marco Verisimo a number 
of years ago your number of k-points must be a multiple of three, which it is, 
but the shift by 0.5, 0.5 is driving the sampling away from

RE: [SIESTA-L] Band structure of MoSe2

[Salvador Barraza-Lopez]

The only thing that is evident to me at this moment is that you are avoiding 
the K-points in your k-point sampling; as indicated by Marco Verisimo a number 
of years ago your number of k-points must be a multiple of three, which it is, 
but the shift by 0.5, 0.5 is driving the sampling away from the K-points and 
avoiding them... Hopefully bringing the shifts to 0.0 0.0 0.0 solves the 
differential, or the missing of the K-point on the conduction band.


I would work on the Mo pseudo a little more; and have you checked the effect of 
the basis size as well? Do your pseudos give you a reasonable bulk band 
structure?


Best regards,

-Salvador



From: siesta-l-requ...@uam.es siesta-l-requ...@uam.es on behalf of Xiaoming 
Wang xw...@rci.rutgers.edu
Sent: Thursday, April 30, 2015 7:23 PM
To: siesta-l@uam.es
Subject: [SIESTA-L] Band structure of MoSe2

Dear Siesta users,

Recently, I’m trying to  calculate the band structure of monolayer MoSe2.  
However, when I plotting the bands, the band curves at K point are not at 
maximum or minimum, which should be. And there seems a non-differential point 
at K along the bands. The band structure of MoSe2 is attached, the 
non-differential point is more obvious at the lowest two bands shown in the 
Fig. Both LDA and PBE functionals give this strange phenomenon. I have tried to 
tune many parameters, but failed to get good result. Can anyone help me with 
the problem?
By the way, I have tried pseudopotentials from Siesta website and from 
http://charter.cnf.cornell.edu/https://urldefense.proofpoint.com/v2/url?u=http-3A__charter.cnf.cornell.edu_d=AwMFAgc=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQm=NaDRSvcZImjiuqSJSGFoSEOGLfumFBd6_fRZa0Hs0Bss=UQq2ZNZfUJL5kmP2F3B0GlcPmhnT4dJuFcGi_NHsl2Qe=,
 and also used the recently published pps of Comput. Mater. Sci. , 98 (2015) 
372-389. I also changed the energshift, meshcutoff, and k point mesh. But none 
of them can resolve the problem. Below are the input files for relaxation and 
band structure calculations. Any comment or advice are highly appreciated.


fdf for relaxation:

# General System Descriptors

SystemName  mose2
SystemLabel mose2

NumberOfAtoms   3
NumberOfSpecies 2

%block ChemicalSpeciesLabel
1  42  Mo
2  34  Se
%endblock ChemicalSpeciesLabel

PAO.EnergyShift 50 meV
PAO.BasisSize   DZP

# Structure and K-sampling

LatticeConstant 1.00 Ang
%block LatticeParameters
3.25 3.25 20.00 90. 90. 120.
%endblock LatticeParameters

AtomicCoordinatesFormat Fractional
AtomicCoorFormatOut Ang
%block AtomicCoordinatesAndAtomicSpecies
   0.3   0.66670   0.505669950  1
   0.7   0.0   0.625537344  2
   0.7   0.0   0.385811946  2
%endblock AtomicCoordinatesAndAtomicSpecies

%block kgrid_Monkhorst_Pack
  12  0  0  0.5
   0 12  0  0.5
   0  0  1  0.0
%endblock kgrid_Monkhorst_Pack

# DFT

XC.functional   LDA
XC.authors  CA
SpinPolarized   false
MaxSCFIterations200
DM.MixingWeight 0.25
DM.NumberPulay  3
DM.Tolerance1.d-5
MeshCutoff  300 Ry
SolutionMethod  diagon
ElectronicTemperature   300.0 K

# MD and Relaxations

MD.TypeOfRunCG
MD.VariableCell T
MD.MaxForceTol  0.01 eV/Ang
MD.MaxStressTol 0.1 GPa
MD.NumCGsteps   200
MD.MaxCGDispl   0.1 Ang
MD.RelaxCellOnlyF

%block GeometryConstraints
   stress 3 4 5 6
%endblock GeometryConstraints

# Output options

WriteCoorInitialtrue
WriteCoorStep   true
WriteForces true
WriteKpointsfalse
WriteEigenvaluesfalse
WriteKbands false
WriteBands  false
WriteMullikenPop0
WriteWaveFunction   false
WriteCoorXmol   true
WriteCoorCerius false
WriteMDCoorXmol true
WriteMDhistory  true
WriteMDXmol true
WriteDM true

fdf for band structure:
# General System Descriptors

SystemName mose2
SystemLabel mose2

NumberOfAtoms   3
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1  42  Mo
2  34  Se
%endblock ChemicalSpeciesLabel

PAO.BasisSize   DZP
PAO.EnergyShift 50 meV

# Structure and K-sampling

LatticeConstant 1.00 Ang
%block LatticeParameters
3.16 3.16 13.00 90. 90. 120.
%endblock LatticeParameters

AtomicCoordinatesFormat Fractional
AtomicCoorFormatOut Ang
%block AtomicCoordinatesAndAtomicSpecies
   0.3   0.66670   0.505669950  1
   0.7   0.0   0.625537344  2
   0.7   0.0   0.385811946  2
%endblock AtomicCoordinatesAndAtomicSpecies

%block kgrid_Monkhorst_Pack
  24  0  0  0.5
   0 24  0  0.5
   0  0  1  0.0
%endblock kgrid_Monkhorst_Pack

# DFT

XC.functional   LDA
XC.authors  CA
SpinPolarized

RE: [SIESTA-L] Band structure of MoSe2

[Xiaoming Wang]

Hi  Salvador,

 

Thanks for your reply. Changing  the shifts to 0.0 0.0 0.0 actually can't
solve the problem. And I have also checked the basis sizes of SZ, SZP, DZ
but not beyond DZP,  the 'non-differential' point still exists. By the way,
I have rechecked the band structure, the 'non-differential' points can
actually also be observed at M(0.0, 0.5, 0.0) k-point,  but not as obvious
as that of K(0.333, 0.333, 0.0) point.

I havn't tried the bulk band structure yet.

 

Best regards,

 

Xiaoming

 

From: siesta-l-requ...@uam.es [mailto:siesta-l-requ...@uam.es] On Behalf Of
Salvador Barraza-Lopez
Sent: Thursday, April 30, 2015 9:46 PM
To: siesta-l@uam.es
Subject: RE: [SIESTA-L] Band structure of MoSe2

 

The only thing that is evident to me at this moment is that you are avoiding
the K-points in your k-point sampling; as indicated by Marco Verisimo a
number of years ago your number of k-points must be a multiple of three,
which it is, but the shift by 0.5, 0.5 is driving the sampling away from the
K-points and avoiding them... Hopefully bringing the shifts to 0.0 0.0 0.0
solves the differential, or the missing of the K-point on the conduction
band.

 

I would work on the Mo pseudo a little more; and have you checked the effect
of the basis size as well? Do your pseudos give you a reasonable bulk band
structure?

 

Best regards,

-Salvador

 

  _  

From: siesta-l-requ...@uam.es mailto:siesta-l-requ...@uam.es
siesta-l-requ...@uam.es mailto:siesta-l-requ...@uam.es  on behalf of
Xiaoming Wang xw...@rci.rutgers.edu mailto:xw...@rci.rutgers.edu 
Sent: Thursday, April 30, 2015 7:23 PM
To: siesta-l@uam.es mailto:siesta-l@uam.es 
Subject: [SIESTA-L] Band structure of MoSe2 

 

Dear Siesta users,

 

Recently, I'm trying to  calculate the band structure of monolayer MoSe2.
However, when I plotting the bands, the band curves at K point are not at
maximum or minimum, which should be. And there seems a non-differential
point at K along the bands. The band structure of MoSe2 is attached, the
non-differential point is more obvious at the lowest two bands shown in the
Fig. Both LDA and PBE functionals give this strange phenomenon. I have tried
to tune many parameters, but failed to get good result. Can anyone help me
with the problem? 

By the way, I have tried pseudopotentials from Siesta website and from
http://charter.cnf.cornell.edu/
https://urldefense.proofpoint.com/v2/url?u=http-3A__charter.cnf.cornell.edu
_d=AwMFAgc=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8r=n_Y76F1vumEs9EYNH
N2gzA5FD9jzyPhrzl3eOzxCHIQm=NaDRSvcZImjiuqSJSGFoSEOGLfumFBd6_fRZa0Hs0Bss=U
Qq2ZNZfUJL5kmP2F3B0GlcPmhnT4dJuFcGi_NHsl2Qe= , and also used the recently
published pps of Comput. Mater. Sci. , 98 (2015) 372-389. I also changed the
energshift, meshcutoff, and k point mesh. But none of them can resolve the
problem. Below are the input files for relaxation and band structure
calculations. Any comment or advice are highly appreciated.

 

 

fdf for relaxation:

 

# General System Descriptors

 

SystemName  mose2

SystemLabel mose2

 

NumberOfAtoms   3

NumberOfSpecies 2

 

%block ChemicalSpeciesLabel

1  42  Mo

2  34  Se

%endblock ChemicalSpeciesLabel

 

PAO.EnergyShift 50 meV

PAO.BasisSize   DZP

 

# Structure and K-sampling

 

LatticeConstant 1.00 Ang

%block LatticeParameters

3.25 3.25 20.00 90. 90. 120.

%endblock LatticeParameters

 

AtomicCoordinatesFormat Fractional

AtomicCoorFormatOut Ang

%block AtomicCoordinatesAndAtomicSpecies

   0.3   0.66670   0.505669950  1

   0.7   0.0   0.625537344  2

   0.7   0.0   0.385811946  2

%endblock AtomicCoordinatesAndAtomicSpecies

 

%block kgrid_Monkhorst_Pack

  12  0  0  0.5

   0 12  0  0.5

   0  0  1  0.0

%endblock kgrid_Monkhorst_Pack

 

# DFT

 

XC.functional   LDA

XC.authors  CA

SpinPolarized   false

MaxSCFIterations200 

DM.MixingWeight 0.25

DM.NumberPulay  3

DM.Tolerance1.d-5

MeshCutoff  300 Ry

SolutionMethod  diagon

ElectronicTemperature   300.0 K

 

# MD and Relaxations

 

MD.TypeOfRunCG

MD.VariableCell T

MD.MaxForceTol  0.01 eV/Ang

MD.MaxStressTol 0.1 GPa

MD.NumCGsteps   200

MD.MaxCGDispl   0.1 Ang

MD.RelaxCellOnlyF

 

%block GeometryConstraints

   stress 3 4 5 6

%endblock GeometryConstraints

 

# Output options

 

WriteCoorInitialtrue

WriteCoorStep   true

WriteForces true

WriteKpointsfalse

WriteEigenvaluesfalse

WriteKbands false

WriteBands  false

WriteMullikenPop0

WriteWaveFunction   false

WriteCoorXmol   true

WriteCoorCerius false

WriteMDCoorXmol true

WriteMDhistory  true

WriteMDXmol true

WriteDM true

 

fdf

[SIESTA-L] Band structure of MoSe2

[Xiaoming Wang]

Dear Siesta users,

 

Recently, I'm trying to  calculate the band structure of monolayer MoSe2.
However, when I plotting the bands, the band curves at K point are not at
maximum or minimum, which should be. And there seems a non-differential
point at K along the bands. The band structure of MoSe2 is attached, the
non-differential point is more obvious at the lowest two bands shown in the
Fig. Both LDA and PBE functionals give this strange phenomenon. I have tried
to tune many parameters, but failed to get good result. Can anyone help me
with the problem? 

By the way, I have tried pseudopotentials from Siesta website and from
http://charter.cnf.cornell.edu/, and also used the recently published pps of
Comput. Mater. Sci. , 98 (2015) 372-389. I also changed the energshift,
meshcutoff, and k point mesh. But none of them can resolve the problem.
Below are the input files for relaxation and band structure calculations.
Any comment or advice are highly appreciated.

 

 

fdf for relaxation:

 

# General System Descriptors

 

SystemName  mose2

SystemLabel mose2

 

NumberOfAtoms   3

NumberOfSpecies 2

 

%block ChemicalSpeciesLabel

1  42  Mo

2  34  Se

%endblock ChemicalSpeciesLabel

 

PAO.EnergyShift 50 meV

PAO.BasisSize   DZP

 

# Structure and K-sampling

 

LatticeConstant 1.00 Ang

%block LatticeParameters

3.25 3.25 20.00 90. 90. 120.

%endblock LatticeParameters

 

AtomicCoordinatesFormat Fractional

AtomicCoorFormatOut Ang

%block AtomicCoordinatesAndAtomicSpecies

   0.3   0.66670   0.505669950  1

   0.7   0.0   0.625537344  2

   0.7   0.0   0.385811946  2

%endblock AtomicCoordinatesAndAtomicSpecies

 

%block kgrid_Monkhorst_Pack

  12  0  0  0.5

   0 12  0  0.5

   0  0  1  0.0

%endblock kgrid_Monkhorst_Pack

 

# DFT

 

XC.functional   LDA

XC.authors  CA

SpinPolarized   false

MaxSCFIterations200 

DM.MixingWeight 0.25

DM.NumberPulay  3

DM.Tolerance1.d-5

MeshCutoff  300 Ry

SolutionMethod  diagon

ElectronicTemperature   300.0 K

 

# MD and Relaxations

 

MD.TypeOfRunCG

MD.VariableCell T

MD.MaxForceTol  0.01 eV/Ang

MD.MaxStressTol 0.1 GPa

MD.NumCGsteps   200

MD.MaxCGDispl   0.1 Ang

MD.RelaxCellOnlyF

 

%block GeometryConstraints

   stress 3 4 5 6

%endblock GeometryConstraints

 

# Output options

 

WriteCoorInitialtrue

WriteCoorStep   true

WriteForces true

WriteKpointsfalse

WriteEigenvaluesfalse

WriteKbands false

WriteBands  false

WriteMullikenPop0

WriteWaveFunction   false

WriteCoorXmol   true

WriteCoorCerius false

WriteMDCoorXmol true

WriteMDhistory  true

WriteMDXmol true

WriteDM true

 

fdf for band structure:

# General System Descriptors

 

SystemName mose2

SystemLabel mose2

 

NumberOfAtoms   3

NumberOfSpecies 2

%block ChemicalSpeciesLabel

1  42  Mo

2  34  Se

%endblock ChemicalSpeciesLabel

 

PAO.BasisSize   DZP

PAO.EnergyShift 50 meV

 

# Structure and K-sampling

 

LatticeConstant 1.00 Ang

%block LatticeParameters

3.16 3.16 13.00 90. 90. 120.

%endblock LatticeParameters

 

AtomicCoordinatesFormat Fractional

AtomicCoorFormatOut Ang

%block AtomicCoordinatesAndAtomicSpecies

   0.3   0.66670   0.505669950  1

   0.7   0.0   0.625537344  2

   0.7   0.0   0.385811946  2

%endblock AtomicCoordinatesAndAtomicSpecies

 

%block kgrid_Monkhorst_Pack

  24  0  0  0.5

   0 24  0  0.5

   0  0  1  0.0

%endblock kgrid_Monkhorst_Pack

 

# DFT

 

XC.functional   LDA

XC.authors  CA

SpinPolarized   false

MaxSCFIterations200 

DM.MixingWeight 0.25

DM.NumberPulay  3

DM.Tolerance1.d-5

MeshCutoff  300 Ry

SolutionMethod  diagon

ElectronicTemperature   300.0 K

 

# Output options

 

WriteCoorInitialtrue

WriteCoorStep   true

WriteForces true

WriteKpointsfalse

WriteEigenvaluesfalse

WriteKbands false

WriteBands  false

WriteMullikenPop0

WriteWaveFunction   false

WriteCoorXmol   true

WriteCoorCerius false

WriteMDCoorXmol true

WriteMDhistory  true

WriteMDXmol true

WriteDM true

UseStructFile   T

 

BandLinesScale ReciprocalLatticeVectors

 

%block BandLines

1   0.  0. 0.  \Gamma

70  0.  0.5000 0.  M

40  0.  0. 0.  K

80  0.  0. 0.  \Gamma

%endblock BandLines

 

 

 

 

Best regards,

 

Xiaoming Wang

IAMDN, 

RE: [SIESTA-L] Band structure calculation

[BingHuang]

Hi,
The band structure of 2x2 supercell is definitely different from that of 1x1 
unit cell. In the supercell case, band structure is folded.  Please have a look 
at the article EPL, 107 (2014) 27006 
(http://iopscience.iop.org/0295-5075/107/2/27006)
Best regards,Bing

From: argo.nurbaw...@gmail.com
To: siesta-l@uam.es
Date: Mon, 16 Mar 2015 18:11:57 +0800
Subject: Re: [SIESTA-L] Band structure calculation




  
  


Hi Barnali



your structures are different from one another.



In your unit cell structure C-C bond is 1.56 Ang, while in your 2x2 supercell 
the C-C bond is 1.42 Ang.



You need to relax the structure correctly first (together with the lattice 
vectors), then the two bands should be the same.



Good luck.



Argo.



On Mon, 2015-03-16 at 15:15 +0530, Barnali Bhattacharya wrote:

Dear all,



I have calculated the band structure for graphene unit cell containing two 
atoms which is accurate one. But when I am trying to calculate the band 
structure of 2*2 graphene super cell the band structure look different . But 
this should not be expected, because the band structure for unit cell and super 
cell should be same. 



Could anybody guide me why I get different band structure for same system
(unit cell and supercell)?
Could anybody help me to solve this problem?





Here I have attached the input file for graphene unit cell and graphene 2*2 
super cell for detils information and the jpg file.





Thanks in advance,
Barnali Bhattacharya,

Assam university,India
  

Re: [SIESTA-L] Band structure calculation

[Argo]

Hi Barnali

your structures are different from one another.

In your unit cell structure C-C bond is 1.56 Ang, while in your 2x2
supercell the C-C bond is 1.42 Ang.

You need to relax the structure correctly first (together with the
lattice vectors), then the two bands should be the same.

Good luck.

Argo.

On Mon, 2015-03-16 at 15:15 +0530, Barnali Bhattacharya wrote:
 Dear all,
 
 I have calculated the band structure for graphene unit cell containing
 two atoms which is accurate one. But when I am trying to calculate the
 band structure of 2*2 graphene super cell the band structure look
 different . But this should not be expected, because the band
 structure for unit cell and super cell should be same. 
 
 
 Could anybody guide me why I get different band structure for same system
 (unit cell and supercell)?
 Could anybody help me to solve this problem?
 
 
 
 Here I have attached the input file for graphene unit cell and
 graphene 2*2 super cell for detils information and the jpg file.
 
 
 
 
 Thanks in advance,
 Barnali Bhattacharya,
 
 Assam university,India

Re: [SIESTA-L] Band Structure - How build the block for the Orthorhombic system?

[I. Camps]

Hello Guilherme,

In general the path is not for your sample. You chose the path depending on
the symmetry of your sample.

My advises:
-) take a look in Solid State Physics books (Kittel:
https://archive.org/details/IntroductionToSolidStatePhysics; Aschroft:
http://www.amazon.com/Solid-State-Physics-Neil-Ashcroft/dp/0030839939)
-) search for papers that do calculations for the same sample/symmetry as
yours. In this way you will get a good (already used) path but will
continuos without getting the physics behind this type of calculation
(electronic band calculation).

Regards,

Camps

On Monday, February 16, 2015, Guilherme Maia Sawyer guisaw...@yahoo.com.br
wrote:

 Hi Camps,

 I found other example... but still I couldn't understand exactly this
 positions...
 This is for the Silicon
 %block BandLines
 1 1.5 1.5 0.0 K # Begin at K
 38 0.0 0.0 0.0 \Gamma # 38 points from K to Gamma
 36 0.0 2.0 0.0 X # 36 points from Gamma to X
 18 1.0 2.0 0.0 W # 18 points from X to W
 26 1.0 1.0 1.0 L # 26 points from W to L
 31 0.0 0.0 0.0 \Gamma # 31 points from L to Gamma
 %endblock BandLines
 How I can find the best path for my sample?!

 The only position I understand it's for Gamma...  and why this path?... I
 gave a quick read in the paper that you told me and didn't find... but I'll
 read again !!

 Thanks for the help!

 ___
 Guilherme Maia Santos

 *Se as pessoas são boas só por temerem o castigo e almejarem uma
 recompensa,*
 * então realmente somos um grupo muito desprezível.*
 *(Albert Einstein)*


   Em Segunda-feira, 16 de Fevereiro de 2015 16:02, I. Camps 
 ica...@gmail.com javascript:_e(%7B%7D,'cvml','ica...@gmail.com');
 escreveu:


 Hello Guilherme,
 Take a look in this link:
 en.Wikipedia.org/wiki/Brillouin_zone
 http://en.wikipedia.org/wiki/Brillouin_zone
 This is based in the paper Comp. Mat. Sci. 49 (2) 299-312, DOI:
 10.1016/j.commatsci.2010.05.010
 Or any good Solid State Book.
 There is also a server named Bilbao Crystallographic Server:
 www.cryst.ehu.es
 Good reading.

 On Mon, Feb 16, 2015, 19:36 Guilherme Maia Sawyer guisaw...@yahoo.com.br
 javascript:_e(%7B%7D,'cvml','guisaw...@yahoo.com.br'); wrote:

 Hi all,

 I'm trying to plot Band Structure using the gnuband (Util from Siesta)...
 But I have one doubt about %block BandLines that we have to write in the
 .fdf file...
 According the Siesta Manual, we usually write along the high-symmetry
 directions... but where I can find it?!
 In the manual :
 %block BandLines
 1 1.000 1.000 1.000 L # Begin at L
 20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
 25 2.000 0.000 0.000 X # 25 points from gamma to X
 30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
 %endblock BandLines
 This is for an FCC lattice... I tried to find this values for this lattice
 just to understand how build for my system... but nothing...
 My system it's a Orthorhombic...for this one.. which is the high-symmetry
 directions?!

 Thanks!





-- 

[]'s,

@mps

Re: [SIESTA-L] Band Structure - How build the block for the Orthorhombic system?

[Alex Pak]

Do you know the Space Group of your material? As Camps mentioned in a
previous email, the Bilbao Crystallographic Server is a good reference for
finding out which high-symmetry points in k-space you'd like to probe to
understand the electronic band structure.  Note that rather than sampling
the entire Brillouin zone, you are looking at the dispersion along
high-symmetry paths.

On Tue, Feb 17, 2015 at 2:52 PM, I. Camps ica...@gmail.com wrote:

 Hello Guilherme,

 In general the path is not for your sample. You chose the path depending
 on the symmetry of your sample.

 My advises:
 -) take a look in Solid State Physics books (Kittel:
 https://archive.org/details/IntroductionToSolidStatePhysics; Aschroft:
 http://www.amazon.com/Solid-State-Physics-Neil-Ashcroft/dp/0030839939)
 -) search for papers that do calculations for the same sample/symmetry as
 yours. In this way you will get a good (already used) path but will
 continuos without getting the physics behind this type of calculation
 (electronic band calculation).

 Regards,

 Camps

 On Monday, February 16, 2015, Guilherme Maia Sawyer 
 guisaw...@yahoo.com.br wrote:

 Hi Camps,

 I found other example... but still I couldn't understand exactly this
 positions...
 This is for the Silicon
 %block BandLines
 1 1.5 1.5 0.0 K # Begin at K
 38 0.0 0.0 0.0 \Gamma # 38 points from K to Gamma
 36 0.0 2.0 0.0 X # 36 points from Gamma to X
 18 1.0 2.0 0.0 W # 18 points from X to W
 26 1.0 1.0 1.0 L # 26 points from W to L
 31 0.0 0.0 0.0 \Gamma # 31 points from L to Gamma
 %endblock BandLines
 How I can find the best path for my sample?!

 The only position I understand it's for Gamma...  and why this path?... I
 gave a quick read in the paper that you told me and didn't find... but I'll
 read again !!

 Thanks for the help!

 ___
 Guilherme Maia Santos

 *Se as pessoas são boas só por temerem o castigo e almejarem uma
 recompensa,*
 * então realmente somos um grupo muito desprezível.*
 *(Albert Einstein)*


   Em Segunda-feira, 16 de Fevereiro de 2015 16:02, I. Camps 
 ica...@gmail.com escreveu:


 Hello Guilherme,
 Take a look in this link:
 en.Wikipedia.org/wiki/Brillouin_zone
 http://en.wikipedia.org/wiki/Brillouin_zone
 This is based in the paper Comp. Mat. Sci. 49 (2) 299-312, DOI:
 10.1016/j.commatsci.2010.05.010
 Or any good Solid State Book.
 There is also a server named Bilbao Crystallographic Server:
 www.cryst.ehu.es
 Good reading.

 On Mon, Feb 16, 2015, 19:36 Guilherme Maia Sawyer guisaw...@yahoo.com.br
 wrote:

 Hi all,

 I'm trying to plot Band Structure using the gnuband (Util from Siesta)...
 But I have one doubt about %block BandLines that we have to write in the
 .fdf file...
 According the Siesta Manual, we usually write along the high-symmetry
 directions... but where I can find it?!
 In the manual :
 %block BandLines
 1 1.000 1.000 1.000 L # Begin at L
 20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
 25 2.000 0.000 0.000 X # 25 points from gamma to X
 30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
 %endblock BandLines
 This is for an FCC lattice... I tried to find this values for this
 lattice just to understand how build for my system... but nothing...
 My system it's a Orthorhombic...for this one.. which is the high-symmetry
 directions?!

 Thanks!





 --

 []'s,

 @mps




-- 

*Alexander J. Pak*

Graduate Research Assistant - The Hwang Group

Department of Chemical Engineering
Cockrell School of Engineering

The University of Texas at Austin
1 University Station, C0400
Austin, Texas 78712

CPE 4.422 | O: (512) 471-1839

M: (917) 637-0413 | a...@utexas.edu


 a...@utexas.edu

[SIESTA-L] Band Structure - How build the block for the Orthorhombic system?

[Guilherme Maia Sawyer]

 Hi all,
I'm trying to plot Band Structure using the gnuband (Util from Siesta)...
But I have one doubt about %block BandLines that we have to write in the .fdf 
file...
According the Siesta Manual, we usually write along the high-symmetry 
directions... but where I can find it?! 
In the manual :
%block BandLines 
1 1.000 1.000 1.000 L # Begin at L
20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
25 2.000 0.000 0.000 X # 25 points from gamma to X
30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
%endblock BandLinesThis is for an FCC lattice... I tried to find this values 
for this lattice just to understand how build for my system... but nothing...My 
system it's a Orthorhombic...for this one.. which is the high-symmetry 
directions?!
Thanks! 

Re: [SIESTA-L] Band Structure - How build the block for the Orthorhombic system?

[I. Camps]

Hello Guilherme,

Take a look in this link:
en.Wikipedia.org/wiki/Brillouin_zone

This is based in the paper Comp. Mat. Sci. 49 (2) 299-312, DOI:
10.1016/j.commatsci.2010.05.010

Or any good Solid State Book.

There is also a server named Bilbao Crystallographic Server:
www.cryst.ehu.es

Good reading.

On Mon, Feb 16, 2015, 19:36 Guilherme Maia Sawyer guisaw...@yahoo.com.br
wrote:

 Hi all,

 I'm trying to plot Band Structure using the gnuband (Util from Siesta)...
 But I have one doubt about %block BandLines that we have to write in the
 .fdf file...
 According the Siesta Manual, we usually write along the high-symmetry
 directions... but where I can find it?!
 In the manual :
 %block BandLines
 1 1.000 1.000 1.000 L # Begin at L
 20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
 25 2.000 0.000 0.000 X # 25 points from gamma to X
 30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
 %endblock BandLines
 This is for an FCC lattice... I tried to find this values for this lattice
 just to understand how build for my system... but nothing...
 My system it's a Orthorhombic...for this one.. which is the high-symmetry
 directions?!

 Thanks!

Re: [SIESTA-L] Band Structure - How build the block for the Orthorhombic system?

[Guilherme Maia Sawyer]

Hi Camps, 

I found other example... but still I couldn't understand exactly this 
positions...
This is for the Silicon%block BandLines
1 1.5 1.5 0.0 K # Begin at K
38 0.0 0.0 0.0 \Gamma # 38 points from K to Gamma
36 0.0 2.0 0.0 X # 36 points from Gamma to X
18 1.0 2.0 0.0 W # 18 points from X to W
26 1.0 1.0 1.0 L # 26 points from W to L
31 0.0 0.0 0.0 \Gamma # 31 points from L to Gamma
%endblock BandLinesHow I can find the best path for my sample?!
The only position I understand it's for Gamma...  and why this path?... I gave 
a quick read in the paper that you told me and didn't find... but I'll read 
again !!

Thanks for the help! ___Guilherme Maia Santos
Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, 
então realmente somos um grupo muito desprezível.(Albert Einstein) 

 Em Segunda-feira, 16 de Fevereiro de 2015 16:02, I. Camps 
ica...@gmail.com escreveu:
   

 Hello Guilherme,Take a look in this link:
en.Wikipedia.org/wiki/Brillouin_zoneThis is based in the paper Comp. Mat. Sci. 
49 (2) 299-312, DOI: 10.1016/j.commatsci.2010.05.010Or any good Solid State 
Book.There is also a server named Bilbao Crystallographic Server: 
www.cryst.ehu.es Good reading.

On Mon, Feb 16, 2015, 19:36 Guilherme Maia Sawyer guisaw...@yahoo.com.br 
wrote:

 Hi all,
I'm trying to plot Band Structure using the gnuband (Util from Siesta)...
But I have one doubt about %block BandLines that we have to write in the .fdf 
file...
According the Siesta Manual, we usually write along the high-symmetry 
directions... but where I can find it?! 
In the manual :
%block BandLines 
1 1.000 1.000 1.000 L # Begin at L
20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
25 2.000 0.000 0.000 X # 25 points from gamma to X
30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
%endblock BandLinesThis is for an FCC lattice... I tried to find this values 
for this lattice just to understand how build for my system... but nothing...My 
system it's a Orthorhombic...for this one.. which is the high-symmetry 
directions?!
Thanks! 



   

Re: [SIESTA-L] Band Structure of Supercell

[Michael Shin]

Hello,
Can any one explain me how to plot the band structure of 2x2x1 supercell of 
graphene.
I am able to do it for 1x1x1 and I have the Dirac cone, but I dont see the band 
strucrure when I use 2x2x1 supercell.
Can some one help me and share an example .fdf file to show how to have the 
same band structure when we 1x1x1 and 2x2x1 supercells.
Thank you in adavance.
Mic




On Saturday, March 15, 2014 9:51 PM, Suman Chowdhury 
sumanchowdhur...@gmail.com wrote:
 
Dear all,
How can I get a good band structure when my unit cell is large?

-- 

Junior research fellow
 Dept. of Physics,
 University of Calcutta
 Kolkata- 79, West Bengal, India.
 Ph no-+91-9830512232

[SIESTA-L] Band Structure

[Suman Chowdhury]

Dear all,
How can I get a good band structure when my unit cell is large?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure

[Mostafa Shabani]

WriteBands  T



On Thu, Feb 20, 2014 at 8:18 PM, Suman Chowdhury sumanchowdhur...@gmail.com
 wrote:

 Dear all,
 To plot the band structure which is to be set true, WriteBands or
 WriteKBands or both.

 --



 *Junior research fellow  Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*

[SIESTA-L] Band Structure

[Suman Chowdhury]

Dear all,
To plot the band structure which is to be set true, WriteBands or
WriteKBands or both.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] band structure vs cell size

[Huang Bing]

Hi,
I'm using Siesta to calculate band structure of bulk gold. It's expected to
find one relative band gap (in which fermi level lies. PS: this gap
supports an occupied Shockley surface state) along GL line (corresponding
to [111] direction) in reciprocal space. I did find one when setting the
cell size to 1x1x1 (primitive cell containing only one atom), but failed
when setting cell size to 2x2x2 (primitive cell containing 8 atoms), see
the attachment for detail. I don't quite understand why the relative gap
vanish near fermi level, one consequence of which seems to be the
disappearance of the previously-mentioned Shockley surface state. Can
anyone explain this?

Re: [SIESTA-L] band structure vs cell size

[venkatesh chandragiri]

Hi,

In 2x2x2 cell, the band folding effects in a Brillouin Zone plays a role on
the arrangement of band structure due to increased cell sizes...this may
give clue to explain the absent of gap in 2x2x2 cell

venkatesh.


On Sat, Sep 7, 2013 at 6:58 PM, Huang Bing hbdft2...@gmail.com wrote:

 Hi,
 I'm using Siesta to calculate band structure of bulk gold. It's expected
 to find one relative band gap (in which fermi level lies. PS: this gap
 supports an occupied Shockley surface state) along GL line (corresponding
 to [111] direction) in reciprocal space. I did find one when setting the
 cell size to 1x1x1 (primitive cell containing only one atom), but failed
 when setting cell size to 2x2x2 (primitive cell containing 8 atoms), see
 the attachment for detail. I don't quite understand why the relative gap
 vanish near fermi level, one consequence of which seems to be the
 disappearance of the previously-mentioned Shockley surface state. Can
 anyone explain this?




-- 
Ch. Venkatesh,
C/o. Prof. V. Srinivas,
Department of Physics  Meteorology,
IIT Kharagpur.
ph: +919445909693

Re: [SIESTA-L] band structure vs cell size

[Bing Huang]

Hi, venkatesh
Thanks for your immediate reply.
Imagine sending an electron with energy within the gap (in the case of 
1x1x1 primitive cell) from vacuum towards the Au(111) surface (this 
surface is perpendicular to [111] direction), the electron cannot 
propagate inside the crystal and must be reflected backwards. Further, 
if the energy of incoming electron is below the vacuum level (i.e., work 
function), the electron cannot escape and is therefore confined. Now if 
we switch to the case of 2x2x2 primitive cell, then we get the opposite 
conclusion: the electron won't be confined! I suppose this is apparently 
not the case.



On 09/07/2013 09:53 PM, venkatesh chandragiri wrote:

Hi,

In 2x2x2 cell, the band folding effects in a Brillouin Zone plays a 
role on the arrangement of band structure due to increased cell 
sizes...this may give clue to explain the absent of gap in 2x2x2 cell


venkatesh.


On Sat, Sep 7, 2013 at 6:58 PM, Huang Bing hbdft2...@gmail.com 
mailto:hbdft2...@gmail.com wrote:


Hi,
I'm using Siesta to calculate band structure of bulk gold. It's
expected to find one relative band gap (in which fermi level lies.
PS: this gap supports an occupied Shockley surface state) along GL
line (corresponding to [111] direction) in reciprocal space. I did
find one when setting the cell size to 1x1x1 (primitive cell
containing only one atom), but failed when setting cell size to
2x2x2 (primitive cell containing 8 atoms), see the attachment for
detail. I don't quite understand why the relative gap vanish near
fermi level, one consequence of which seems to be the
disappearance of the previously-mentioned Shockley surface state.
Can anyone explain this?




--
Ch. Venkatesh,
C/o. Prof. V. Srinivas,
Department of Physics  Meteorology,
IIT Kharagpur.
ph: +919445909693

Re: [SIESTA-L] Band structure and Fermi velocity

[Michael Shin]

Hello,
I have some basic questions about the band structure, e.g., graphene.
Plz, see the attached input file (.fdf) and the .bands file generated by 
siesta. The dispersion agrees with the previous work. Now I want to calculate 
the Fermi velcity of Dirac electrons. I can see a linear dispersion around K.
1. How can I use the .bnds file to calculte the Fermi velocoity. Plz, use the 
attached file and explain me. I never did it and its very crucial, minor 
mistake can give me very bad result
2. When I use a big supercell then the band structure of this supercell is 
different from the promitive graphene. How can I reproduce the band structure 
of primitive form the supercell. In principle the band structures should be the 
same except the number of bands.

Regards,
Mic




 From: I. Camps ica...@gmail.com
To: somayeh fotohi somayehfot...@yahoo.com; siesta-l@uam.es 
siesta-l@uam.es 
Sent: Monday, July 29, 2013 3:19 PM
Subject: Re: [SIESTA-L] systemlable.band.up and systemlable.band.down
 


Dear  Somayeh,


Attached is a modified version of gnubands program (I called gnuband_spin). It 
is capable to produce two separate files for the spin up/down bands.

Usage: ./gnubands_spin input_file output_up output_down, were: 

input_file: is you band file

output_up: is the desired name for the file with the bands for the spin up 
configuration 

output_down: is the desired name for the file with the bands for the spin 
down configuration


What I did was to duplicate the code in the original gnuband: the first part 
save the UP configuration, and the second w«one, save the DOWN configuration.


Good luck!


On Sun, Jul 28, 2013 at 7:54 AM, somayeh fotohi somayehfot...@yahoo.com wrote:

Somayeh




[]'s,

@mps

Re: [SIESTA-L] Band Structure Results

[apostnik]

 And another things that I want to ask is, how to label the x-axis so
 that
 we get the symmetry label on that (ex. Gamma, M, K etc.)

 I think they are not automatically produced by the Gnubands
 script, but knowing where they are on the abscissa axis
 (that's you who defined the number of k-points between
 the symmetric corner points, right?),
 you can hopefully add them by hand in your favourite plotting routine.

Dear Yuly,
a correction to this:
I think, the last lines in the .bands file
give the direct placement of labels
along the abscissa axis of the plot.

So in the worst case you just add them by hand
at the specified points.

Best regards

Andrei Postnikov

[SIESTA-L] Band Structure Results

[y_kusumawati]

Hallo SIESTA users!

I have run my fdf to get the band structure for graphene and TIO2 Rutile.
I have made the visualization using gnubands and gnuplot. But then, I got
soo many lines. Can anyone informs me why it can be happened? is there
any mistake?
I trie to attach that picture, but it is difficult.

And another things that I want to ask is, how to label the x-axis so that
we get the symmetry label on that (ex. Gamma, M, K etc.)

I have attached the file of bands structure visualization
and here the K-point for graphene
%block Bandlines
1  -0.500   0.000  0.000 M
25  0.000   0.000  0.000 \Gamma
25  0.3329 -0.6658 0.000 K
%endblock BandLines

while for tio2 (rutile, space group 136)
%block Bandlines
1  0.000 0.000 0.000 \Gamma
20 0.000 0.500 0.000 X
25 0.000 0.500 0.500 R
20 0.000 0.000 0.500 Z
25 0.000 0.000 0.000 \Gamma
20 0.500 0.500 0.000 M
25 0.500 0.500 0.500 A
20 0.000 0.000 0.500 Z
%endblock BandLines

Thank you,

Best Regards

Yuly Kusumawati

Laboratory of Computational Chemistry
Institut Teknologi Bandung (ITB)




--

http://www.its.ac.id 

[SIESTA-L] Band Structure

[Pranjal]

Hello,
I'm sorry if this is a repeat question but I went through the forums and
none of the solutions worked.

I am trying to calculate the band structure of Adamantane and it just gives
me lots of straight lines. I've correctly checked the structure and DOS
from it.

My fdf file is below. If someone could please have a look at it, and advice
on how to get the correct dispersive band structure, it would be really a
great help.

Thanks!

Pranjal Bordia
Physics Ph.D.
Stanford University

#
-
# FDF for Adamantane
#
-

SystemName  ada
SystemLabel ada
NumberOfAtoms   26
NumberOfSpecies 2

%block ChemicalSpeciesLabel
 1  6  C
 2  1  H
%endblock ChemicalSpeciesLabel

LatticeConstant 9.42 Ang

%block LatticeVectors
  0.500  0.500  0.000
  0.500  0.000  0.500
  0.500  0.500  0.000
%endblock LatticeVectors

AtomicCoordinatesFormat   ScaledCartesian

%block AtomicCoordinatesAndAtomicSpecies
  0.000   0.000   0.0001   C
  0.000   0.163   0.0001   C
  0.132   0.216   0.0771   C
  0.265   0.163   0.0001   C
  0.265   0.000   0.0001   C
  0.132  -0.053  -0.0771   C
  0.000  -0.053   0.1531   C
  0.132   0.000   0.2311   C
  0.265  -0.053   0.1531   C
  0.132   0.163   0.2321   C
  0.265  -0.170   0.1532   H
  0.361  -0.015   0.2102   H
  0.038   0.200   0.2882   H
 -0.095  -0.038  -0.0562   H
  0.000   0.200  -0.1112   H
 -0.094   0.200   0.0602   H
  0.132   0.332   0.0772   H
  0.360   0.200   0.0562   H
  0.265   0.200  -0.1102   H
  0.360  -0.038  -0.0562   H
  0.132  -0.170  -0.0782   H
  0.132  -0.015  -0.1852   H
  0.000  -0.170   0.1532   H
 -0.094  -0.015   0.2092   H
  0.132  -0.038   0.3312   H
  0.221   0.200   0.2882   H
%endblock AtomicCoordinatesAndAtomicSpecies

# SCF options
MaxSCFIterations   20   # Maximum number of SCF iter
DM.MixingWeight   0.1   # New DM amount for next SCF cycle
DM.Tolerance  1.d-3 # Tolerance in maximum difference
# between input and output DM
DM.UseSaveDM  true  # to use continuation filesB

SolutionMethoddiagon# OrderN or Diagon
ElectronicTemperature  25 meV   # Temp. for Fermi smearing
XC.authors   CA# Parametrization fos xc
MeshCutoff   150. Ry# Mesh cutoff. real space mesh
KgridCutoff  15. Ang
WriteEigenvalues.true.
WriteKbands .true.
WriteBands  .true.

%block BandLines
1  1.000  1.000  1.000  L#
   25  0.000  0.000  0.000  \Gamma   #
   30  2.000  0.000  0.000  X#
   10  2.000  0.500  0.500  U#
   35  0.000  0.000  0.000  \Gamma   #
%endblock BandLines

%block WaveFuncKPoints   # Weights of orbitals for bands in
k-point
 0.000  0.000  0.000  from 1 to 20   # k-point, and bands required.
%endblock WaveFuncKPoints

Re: [SIESTA-L] Band Structure

[Peter Wang]

latticevectors are wrong.
try to use smaller kgrid_cutoff than lattice constant or to use 
kgrid_Monkhorst_Pack instead.
good luck!
From: Pranjal 
Sent: Thursday, February 16, 2012 4:16 PM
To: siesta-l@uam.es 
Subject: [SIESTA-L] Band Structure


Hello,
I'm sorry if this is a repeat question but I went through the forums and none 
of the solutions worked.

I am trying to calculate the band structure of Adamantane and it just gives me 
lots of straight lines. I've correctly checked the structure and DOS from it.

My fdf file is below. If someone could please have a look at it, and advice on 
how to get the correct dispersive band structure, it would be really a great 
help.

Thanks!

Pranjal Bordia
Physics Ph.D. 
Stanford University

# -
# FDF for Adamantane
# -

SystemName  ada
SystemLabel ada
NumberOfAtoms   26
NumberOfSpecies 2

%block ChemicalSpeciesLabel
1  6  C
2  1  H
%endblock ChemicalSpeciesLabel

LatticeConstant 9.42 Ang

%block LatticeVectors
  0.500  0.500  0.000
  0.500  0.000  0.500
  0.500  0.500  0.000
%endblock LatticeVectors

AtomicCoordinatesFormat   ScaledCartesian

%block AtomicCoordinatesAndAtomicSpecies
  0.000   0.000   0.0001   C
  0.000   0.163   0.0001   C
  0.132   0.216   0.0771   C
  0.265   0.163   0.0001   C
  0.265   0.000   0.0001   C
  0.132  -0.053  -0.0771   C
  0.000  -0.053   0.1531   C
  0.132   0.000   0.2311   C
  0.265  -0.053   0.1531   C
  0.132   0.163   0.2321   C
  0.265  -0.170   0.1532   H
  0.361  -0.015   0.2102   H
  0.038   0.200   0.2882   H
-0.095  -0.038  -0.0562   H
  0.000   0.200  -0.1112   H
-0.094   0.200   0.0602   H
  0.132   0.332   0.0772   H
  0.360   0.200   0.0562   H
  0.265   0.200  -0.1102   H
  0.360  -0.038  -0.0562   H
  0.132  -0.170  -0.0782   H
  0.132  -0.015  -0.1852   H
  0.000  -0.170   0.1532   H
-0.094  -0.015   0.2092   H
  0.132  -0.038   0.3312   H
  0.221   0.200   0.2882   H
%endblock AtomicCoordinatesAndAtomicSpecies

# SCF options
MaxSCFIterations   20   # Maximum number of SCF iter
DM.MixingWeight   0.1   # New DM amount for next SCF cycle
DM.Tolerance  1.d-3 # Tolerance in maximum difference
# between input and output DM
DM.UseSaveDM  true  # to use continuation filesB

SolutionMethoddiagon# OrderN or Diagon
ElectronicTemperature  25 meV   # Temp. for Fermi smearing
XC.authors   CA# Parametrization fos xc
MeshCutoff   150. Ry# Mesh cutoff. real space mesh 
KgridCutoff  15. Ang
WriteEigenvalues.true.
WriteKbands .true.
WriteBands  .true.

%block BandLines
1  1.000  1.000  1.000  L#
   25  0.000  0.000  0.000  \Gamma   #
   30  2.000  0.000  0.000  X#
   10  2.000  0.500  0.500  U#
   35  0.000  0.000  0.000  \Gamma   #
%endblock BandLines

%block WaveFuncKPoints   # Weights of orbitals for bands in k-point
0.000  0.000  0.000  from 1 to 20   # k-point, and bands required.
%endblock WaveFuncKPoints

Re: [SIESTA-L] Band Structure

[Zahra Talebi]

hi
can you send the file by name ada.XV for me. 
thanks



From: Peter Wang yunpengw...@live.com
To: siesta-l@uam.es 
Sent: Thursday, February 16, 2012 12:55 PM
Subject: Re: [SIESTA-L] Band Structure


latticevectors are wrong.
try to use smaller kgrid_cutoff than lattice constant or to use 
kgrid_Monkhorst_Pack instead.

good luck!
From: Pranjal 
Sent: Thursday, February 16, 2012 4:16 PM
To: siesta-l@uam.es 
Subject: [SIESTA-L] Band Structure

Hello,
I'm sorry if this is a repeat question but I went through the forums and none 
of the solutions worked.

I am trying to calculate the band structure of Adamantane and it just gives me 
lots of straight lines. I've correctly checked the structure and DOS from it.

My fdf file is below. If someone could please have a look at it, and advice on 
how to get the correct dispersive band structure, it would be really a great 
help.

Thanks!

Pranjal Bordia
Physics Ph.D. 
Stanford University

# -
# FDF for Adamantane
# -

SystemName  ada
SystemLabel ada
NumberOfAtoms   26
NumberOfSpecies 2

%block ChemicalSpeciesLabel
1  6  C
2  1  H
%endblock ChemicalSpeciesLabel

LatticeConstant 9.42 Ang

%block LatticeVectors
  0.500  0.500  0.000
  0.500  0.000  0.500
  0.500  0.500  0.000
%endblock LatticeVectors

AtomicCoordinatesFormat   ScaledCartesian

%block AtomicCoordinatesAndAtomicSpecies
  0.000   0.000   0.000    1   C
  0.000   0.163   0.000    1   C
  0.132   0.216   0.077    1   C
  0.265   0.163   0.000    1   C
  0.265   0.000   0.000    1   C
  0.132  -0.053  -0.077    1   C
  0.000  -0.053   0.153    1   C
  0.132   0.000   0.231    1   C
  0.265  -0.053   0.153    1   C
  0.132   0.163   0.232    1   C
  0.265  -0.170   0.153    2   H
  0.361  -0.015   0.210    2   H
  0.038   0.200   0.288    2   H
-0.095  -0.038  -0.056    2   H
  0.000   0.200  -0.111    2   H
-0.094   0.200   0.060    2   H
  0.132   0.332   0.077    2   H
  0.360   0.200   0.056    2   H
  0.265   0.200  -0.110    2   H
  0.360  -0.038  -0.056    2   H
  0.132  -0.170  -0.078    2   H
  0.132  -0.015  -0.185    2   H
  0.000  -0.170   0.153    2   H
-0.094  -0.015   0.209    2   H
  0.132  -0.038   0.331    2   H
  0.221   0.200   0.288    2   H
%endblock AtomicCoordinatesAndAtomicSpecies

# SCF options
MaxSCFIterations   20   # Maximum number of SCF iter
DM.MixingWeight   0.1   # New DM amount for next SCF cycle
DM.Tolerance  1.d-3 # Tolerance in maximum difference
    # between input and output DM
DM.UseSaveDM  true  # to use continuation filesB

SolutionMethod    diagon    # OrderN or Diagon
ElectronicTemperature  25 meV   # Temp. for Fermi smearing
XC.authors   CA    # Parametrization fos xc
MeshCutoff   150. Ry    # Mesh cutoff. real space mesh 
KgridCutoff  15. Ang
WriteEigenvalues    .true.
WriteKbands .true.
WriteBands  .true.

%block BandLines
    1  1.000  1.000  1.000  L    #
   25  0.000  0.000  0.000  \Gamma   #
   30  2.000  0.000  0.000  X    #
   10  2.000  0.500  0.500  U    #
   35  0.000  0.000  0.000  \Gamma   #
%endblock BandLines

%block WaveFuncKPoints   # Weights of orbitals for bands in k-point
0.000  0.000  0.000  from 1 to 20   # k-point, and bands required.
%endblock WaveFuncKPoints

[SIESTA-L] Band-Structure Analysis

[y_kusumawati]

Dear Siesta users,

I am new in using SIESTA. I want to know about Band-structure analysis.

1. What are the script that we have to write in fdf file to get the
   band-structure?
   If I am not mistaken (in user's guide Siesta 3.1) we have to set:
   - WriteBands true
   - BandlinesScale
   - Write block Bandlines
   - write BandPoints

   Are there anythings we have to write?

2. A don't understand about block BandLines and BandPoints, for example, in
user's giude written:

%block Bandlines
1  1.000 1.000 1.000 L
20 0.000 0.000 0.000 \Gamma
25 2.000 0.000 0.000 X
20 2.000 2.000 2.000 \Gamma
%endblock BandLines

Would you mind to explain me what's the meaning that. I mean what's the
meening in first colom. Colom 2 to 4 I think the cartesian coordinate, is
that right? but can anyone explain more detail about this.

And so do the BandPoints, I don't understand too about the number that is
written in %block BandPoints. Where is I get that number (for % block
BandLines and %block BandPoints).

Thank you for your explanation.

Best Regards

Yuly Kusumawati

Laboratory Computational Chemistry-Institute Technology of Bandung (ITB)
Indonesia.



--

http://www.its.ac.id 

Re: [SIESTA-L] Band-Structure Analysis

[Dr. Ghous Bakhsh Narejo]

Hi,
1, The scripts are available at siesta-l blog. I can send you .fdf files
containing the band structure script as i have archive as well.

2, First column shows the number of sampling points, 2nd-4th column:
crystalline directions, 5th column rep. the crystalline directions names
in a unit cell.

Dr Ghous B Narejo,

Associate Prof.,

El Engg, NED University, Karachi, Pak.

 Dear Siesta users,

 I am new in using SIESTA. I want to know about Band-structure analysis.

 1. What are the script that we have to write in fdf file to get the
   %20band-structure?
If I am not mistaken (in user's guide Siesta 3.1) we have to set:
- WriteBands true
- BandlinesScale
- Write block Bandlines
- write BandPoints

Are there anythings we have to write?

 2. A don't understand about block BandLines and BandPoints, for example,
 in
 user's giude written:

 %block Bandlines
 1  1.000 1.000 1.000 L
 20 0.000 0.000 0.000 \Gamma
 25 2.000 0.000 0.000 X
 20 2.000 2.000 2.000 \Gamma
 %endblock BandLines

 Would you mind to explain me what's the meaning that. I mean what's the
 meening in first colom. Colom 2 to 4 I think the cartesian coordinate, is
 that right? but can anyone explain more detail about this.

 And so do the BandPoints, I don't understand too about the number that is
 written in %block BandPoints. Where is I get that number (for % block
 BandLines and %block BandPoints).

 Thank you for your explanation.

 Best Regards

 Yuly Kusumawati

 Laboratory Computational Chemistry-Institute Technology of Bandung (ITB)
 Indonesia.



 --

 http://www.its.ac.id

[SIESTA-L] Band structure and non-collinear-spin calculation

[isivkov]

Hello,all.

I want to calculate band structure of a system with non-collinear-spin
calculation. But, when I specify options NonCollinear True  and %block
BandLines ... , then the task crashes after finishing SCF loop.
If I remove %block BandLines ..., then task goes normally.

I would like to know what is going on?

[SIESTA-L] band structure

[Magdalena Birowska]

I have performed Spin Polarized calculations. I would like to know how can I
turn on spin down calculations in the file *.bands


Thanks in advance
Magda

Re: [SIESTA-L] band structure

[Barraza-Lopez,Salvador]

Hi Magda, 

For a given k-point, the bands file will have spin up and spin down entries if 
the run was spin-polarized. To see where the spin down entries start, look for 
a sudden jump in the eigenvalues (ie, from large positive values back to 
negative ones) right at the middle of the dataset for any k-point. 

Best regards, 
-Salvador. 

- Original Message -
From: Magdalena Birowska magda.birow...@gmail.com 
To: siesta-l@uam.es 
Sent: Monday, January 17, 2011 6:26:53 AM 
Subject: [SIESTA-L] band structure 

I have performed Spin Polarized calculations. I would like to know how can I 
turn on spin down calculations in the file *.bands 


Thanks in advance 
Magda 




-- 
Salvador Barraza-Lopez 
Postdoctoral Fellow 
School of Physics 
The Georgia Institute of Technology 

Office N205 
837 State Street Atlanta, Georgia 30332-0430 U.S.A 
Tel: (404) 894-0892 Fax: (404) 894-9958 

Re : [SIESTA-L] band structure

[Slimane Haffad]

the first indicated is spin up both in .bands and .EIG 

slimane,

--- En date de : Dim 2.1.11, Juliana Morbec jmor...@yahoo.com.br a écrit :


De: Juliana Morbec jmor...@yahoo.com.br
Objet: [SIESTA-L] band structure
À: siesta-l@uam.es
Date: Dimanche 2 janvier 2011, 20h31


Dear Siesta users,


I have performed spin polarized calculations, and now, I would like to know if 
there is a order of the spin channels (spin up and spin down) in the 
file.bands. 
Please, what is listed first: spin up or spin down?


Thanks in advance!

Juliana M. Morbec
--
Prof. Dr. Juliana M. Morbec      
Theoretical Condensed Matter Physics
Universidade Federal de Alfenas (Federal University of Alfenas - Brazil)
Tel: ++ 55 35 3299 1459
Homepage: http://tinyurl.com/jmorbec
--



  

[SIESTA-L] band-structure of supercell

[Doron Naveh]

Hi there siesters,
I ran into a very basic problem. I'm trying to calculate the 
bandstructure of a slab. For that matter I an illustrate my problem on 
2x2 graphene unit cell.
The \Gamma point of the 2x2 cell gives wrong eigenvalues compared to the 
1x1 cell (a factor of ~4!!) . Is there a rigid shift of the BZ center ?
Here are the lattice vectors/atom position blocks for the 2x2 cell. for 
the primitive cell atom position is 0,0,0.5; 1/3,1/3,0.5 and the lattice 
parameter reduced by half.

Thanks,
-D.

LatticeConstant 4.9200 Ang
%block LatticeVectors
  0.5   0.866025404   0.0
 -0.5   0.866025404   0.0
  0.0   0.0   3.0
%endblock LatticeVectors

AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.0   0.0   0.500 1
0.1   0.1   0.500 1
0.0   0.5   0.500 1
0.1   0.6   0.500 1
0.5   0.0   0.500 1
0.6   0.1   0.500 1
0.5   0.5   0.500 1
0.6   0.6   0.500 1
%endblock AtomicCoordinatesAndAtomicSpecies

BandLinesScale ReciprocalLatticeVectors
%block BandLines
 1  0.000 0.000 0.00 \Gamma
%endblock BandLines

Re: [SIESTA-L] band-structure of supercell

[Ricardo Faccio]

Dear Doron
Remember when you´re working with supercells the 1st Brillouin zone become 
altered, particularlly reduced. So the orignal band structure, based on the 
original 1st BZ, is then folding in the new one. So, what you  are seeing is 
a mixture of bandlines.
In particular for graphene 2x2 supercell diract point is still present at 
(1/3, 1/3, 0), but you can check how Dirac point moves into Gamma point when 
supercells are multiple of three (eg: 3x3 and, 6x6 supercells).

Best regards
Ricardo
-
 Dr. Ricardo Faccio
 Prof. Adjunto de Física
 Mail: Cryssmat-Lab., Cátedra de Física, DETEMA
 Facultad de Química, Universidad de la República
  Av. Gral. Flores 2124, C.C. 1157
  C.P. 11800, Montevideo, Uruguay.
 E-mail: rfac...@fq.edu.uy
 Phone: 598 2 924 98 59
 598 2 929 06 48
 Fax:598 2 9241906
 Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
-
- Original Message - 
From: Doron Naveh na...@cmu.edu

To: siesta-l@uam.es
Sent: Tuesday, May 04, 2010 4:34 PM
Subject: [SIESTA-L] band-structure of supercell



Hi there siesters,
I ran into a very basic problem. I'm trying to calculate the bandstructure 
of a slab. For that matter I an illustrate my problem on 2x2 graphene unit 
cell.
The \Gamma point of the 2x2 cell gives wrong eigenvalues compared to the 
1x1 cell (a factor of ~4!!) . Is there a rigid shift of the BZ center ?
Here are the lattice vectors/atom position blocks for the 2x2 cell. for 
the primitive cell atom position is 0,0,0.5; 1/3,1/3,0.5 and the lattice 
parameter reduced by half.

Thanks,
-D.

LatticeConstant 4.9200 Ang
%block LatticeVectors
  0.5   0.866025404   0.0
 -0.5   0.866025404   0.0
  0.0   0.0   3.0
%endblock LatticeVectors

AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.0   0.0   0.500 1
0.1   0.1   0.500 1
0.0   0.5   0.500 1
0.1   0.6   0.500 1
0.5   0.0   0.500 1
0.6   0.1   0.500 1
0.5   0.5   0.500 1
0.6   0.6   0.500 1
%endblock AtomicCoordinatesAndAtomicSpecies

BandLinesScale ReciprocalLatticeVectors
%block BandLines
 1  0.000 0.000 0.00 \Gamma
%endblock BandLines 

Re: [SIESTA-L] band-structure of supercell

[apostnik]

 The band gap at \Gamma decreases dramatically (factor of ~ 4) when I use
 the 2x2 cell. Since the \Gamma point is not subjected to folding issues,
 is it possible that there is a bug that translate the BZ center?

Dear Doron,
the Gamma point is not affected by folding, true,
so that its corresponding band energies must rest in place,
but
the bands from other k-points get folded
and come into the Gamma of your supercell

Best regards

Andrei Postnikov


 Thanks,
 -D.

 On 5/4/2010 3:47 PM, Ricardo Faccio wrote:
 Dear Doron
 Remember when you´re working with supercells the 1st Brillouin zone
 become altered, particularlly reduced. So the orignal band structure,
 based on the original 1st BZ, is then folding in the new one. So, what
 you  are seeing is a mixture of bandlines.
 In particular for graphene 2x2 supercell diract point is still present
 at (1/3, 1/3, 0), but you can check how Dirac point moves into Gamma
 point when supercells are multiple of three (eg: 3x3 and, 6x6
 supercells).
 Best regards
 Ricardo
 -
  Dr. Ricardo Faccio
  Prof. Adjunto de Física
  Mail: Cryssmat-Lab., Cátedra de Física, DETEMA
  Facultad de Química, Universidad de la República
   Av. Gral. Flores 2124, C.C. 1157
   C.P. 11800, Montevideo, Uruguay.
  E-mail: rfac...@fq.edu.uy
  Phone: 598 2 924 98 59
  598 2 929 06 48
  Fax:598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
 -

 - Original Message - From: Doron Naveh na...@cmu.edu
 To: siesta-l@uam.es
 Sent: Tuesday, May 04, 2010 4:34 PM
 Subject: [SIESTA-L] band-structure of supercell


 Hi there siesters,
 I ran into a very basic problem. I'm trying to calculate the
 bandstructure of a slab. For that matter I an illustrate my problem
 on 2x2 graphene unit cell.
 The \Gamma point of the 2x2 cell gives wrong eigenvalues compared to
 the 1x1 cell (a factor of ~4!!) . Is there a rigid shift of the BZ
 center ?
 Here are the lattice vectors/atom position blocks for the 2x2 cell.
 for the primitive cell atom position is 0,0,0.5; 1/3,1/3,0.5 and the
 lattice parameter reduced by half.
 Thanks,
 -D.

 LatticeConstant 4.9200 Ang
 %block LatticeVectors
   0.5   0.866025404   0.0
  -0.5   0.866025404   0.0
   0.0   0.0   3.0
 %endblock LatticeVectors

 AtomicCoordinatesFormat Fractional
 %block AtomicCoordinatesAndAtomicSpecies
 0.0   0.0   0.500 1
 0.1   0.1   0.500 1
 0.0   0.5   0.500 1
 0.1   0.6   0.500 1
 0.5   0.0   0.500 1
 0.6   0.1   0.500 1
 0.5   0.5   0.500 1
 0.6   0.6   0.500 1
 %endblock AtomicCoordinatesAndAtomicSpecies

 BandLinesScale ReciprocalLatticeVectors
 %block BandLines
  1  0.000 0.000 0.00 \Gamma
 %endblock BandLines

Re: [SIESTA-L] band-structure of supercell

[Doron Naveh]

Dear Andrei  Ricardo,
Thanks for your response.
When using a say 2x2 supercell the only thing that suppose to change is 
the level of degeneracy.
Take the following argument : if the band lines are changed for a double 
cell, than one needs to converge the number of unit cells to get the 
right band structure. this is of course untrue and a Si crystal, say, 
would still have the same bandstructure if we double the number of atoms 
in the unit cell by taking a 2x1 super-cell.
Therefore, the bandstructure of 2x2 graphene cell should look exactly 
the same as a 1x1 cell, given  that the high symmetry points are scaled 
to the size of the BZ of a supercell.
Since \Gamma point is not subjected to any scaling issues, the 
eigenvalues at this point of BZ should remain the same and only the 
degeneracy should increase.

Cheers,
Doron.




On 5/4/2010 5:09 PM, Doron Naveh wrote:

Dear Ricardo,
Thank you! Actually, I get exactly the same results so the problem 
lies in understanding these results. I checked only the difference 
between highest occupied eigenvalue and lowest unoccupied one.

Thanks very much to you and to Andrei P. - and sorry for the sloppiness..
BTW, my parents didn't have the periodic table on their mined when 
they named me ... :-)

Cheers,
Doron.



On 5/4/2010 4:51 PM, Ricardo Faccio wrote:

Dear Boron

Pure graphene has no gap, maybe you're referring to the difference 
between eigenvalues for particular points in the 1BZ.


I'm sending some results for graphene 1x1 and supercell 2x2 
(path:/gamma, M, K, /gamma). Take a look at /Gamma, where eigenvalues 
at -3.2 eV and -7.3 eV keep their energy position. The others 
correspond to the folding into gamma as was commented by Andrei P.


Maybe there are some issues with you convergence. What parameters did 
you use?


Regards

Ricardo



- 


 Dr. Ricardo Faccio
 Prof. Adjunto de Física
 Mail: Cryssmat-Lab., Cátedra de Física, DETEMA
 Facultad de Química, Universidad de la República
  Av. Gral. Flores 2124, C.C. 1157
  C.P. 11800, Montevideo, Uruguay.
 E-mail: rfac...@fq.edu.uy
 Phone: 598 2 924 98 59
 598 2 929 06 48
 Fax:598 2 9241906
 Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
- 


- Original Message - From: Doron Naveh na...@cmu.edu
To: siesta-l@uam.es
Sent: Tuesday, May 04, 2010 5:07 PM
Subject: Re: [SIESTA-L] band-structure of supercell



Hi Ricardo,
Thanks for the prompt response.
I know about the BZ folding, this is the reason why I took the BZ 
center as an example to make my point.
The band gap at \Gamma decreases dramatically (factor of ~ 4) when I 
use the 2x2 cell. Since the \Gamma point is not subjected to folding 
issues, is it possible that there is a bug that translate the BZ 
center?

Thanks,
-D.

On 5/4/2010 3:47 PM, Ricardo Faccio wrote:

Dear Doron
Remember when you´re working with supercells the 1st Brillouin zone 
become altered, particularlly reduced. So the orignal band 
structure, based on the original 1st BZ, is then folding in the new 
one. So, what you  are seeing is a mixture of bandlines.
In particular for graphene 2x2 supercell diract point is still 
present at (1/3, 1/3, 0), but you can check how Dirac point moves 
into Gamma point when supercells are multiple of three (eg: 3x3 
and, 6x6 supercells).

Best regards
Ricardo
- 


 Dr. Ricardo Faccio
 Prof. Adjunto de Física
 Mail: Cryssmat-Lab., Cátedra de Física, DETEMA
 Facultad de Química, Universidad de la República
  Av. Gral. Flores 2124, C.C. 1157
  C.P. 11800, Montevideo, Uruguay.
 E-mail: rfac...@fq.edu.uy
 Phone: 598 2 924 98 59
 598 2 929 06 48
 Fax:598 2 9241906
 Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
- 



- Original Message - From: Doron Naveh na...@cmu.edu
To: siesta-l@uam.es
Sent: Tuesday, May 04, 2010 4:34 PM
Subject: [SIESTA-L] band-structure of supercell



Hi there siesters,
I ran into a very basic problem. I'm trying to calculate the 
bandstructure of a slab. For that matter I an illustrate my 
problem on 2x2 graphene unit cell.
The \Gamma point of the 2x2 cell gives wrong eigenvalues compared 
to the 1x1 cell (a factor of ~4!!) . Is there a rigid shift of the 
BZ center ?
Here are the lattice vectors/atom position blocks for the 2x2 
cell. for the primitive cell atom position is 0,0,0.5; 1/3,1/3,0.5 
and the lattice parameter reduced by half.

Thanks,
-D.

LatticeConstant 4.9200 Ang
%block LatticeVectors
  0.5   0.866025404   0.0
 -0.5   0.866025404   0.0
  0.0   0.0   3.0
%endblock LatticeVectors

AtomicCoordinatesFormat Fractional
%block

Re: [SIESTA-L] Band Structure

[gjgarcia]

Hi.
A few weeks ago I have the same problema that you. I write here that you
need to calculate bands structure

WriteBands  true

BandLinesScale   pi/a

%block Bandlines
1 1.000 1.000 1.000 L
25 0.000 0.000 0.000 \Gama
30 2.000 0.000 0.000 X
10 2.000 0.500 0.500 U
35 0.000 0.000 0.000 \Gama
%endblock block Bandlines

The bands lines can be scaled by pi/a or Recipprocal Lattice Vectors. I
think that it is more easy by ReciprocalLatticeVectors. But I think that
according your data are scaled by pi/a.

In systemlabel.bands are the bandlines. Then, you have to compile gnubands
(utility directory): ./gnubands systemlabel.bands bandsoutput.
Now, you have a file, use this file to plot bands stracture with gnuplots,
xmgrace, sigmaplot, origin, matlab, ect.
Coordinates of k points are at the end of systemlabel.bands and energy
fermi are in the top of file.bands.


As I said above, few weeks ago I had the same problem. I wrote to
L-SIESTA, with the subject Band structure calculations and K-points,
check it. It helps me a lot.




 Dear All,

 I am new user SIESTA. I would like to calculate the band structure 0f C80
 fullerene. Below I have written the input for the band structure and my
 results is showing just the straight line. Can any body tell me the what
 is
 wrong in my input? Please help how to use the X.band file for band
 structure?

 Thanks!
 SC

 %block BandLines
  1 1.000 1.000 1.000 L
 25 0.000 0.000 0.000 \Gama
 30 2.000 0.000 0.000 X
 10 2.000 0.500 0.500 U
 35 0.000 0.000 0.000 \Gama
 %endblock BandLines

 %block WaveFunKPoints
   0.000 0.000 0.000 free 1 to 10
 %endblock WaveFuncKpoints

Re: [SIESTA-L] Band Structure

[sugata chowdhury]

Dear Garcia,

Thank you for your help.

Thanks!
SC

On Thu, Jan 28, 2010 at 2:35 PM, gjgar...@ujaen.es wrote:

 Hi.
 A few weeks ago I have the same problema that you. I write here that you
 need to calculate bands structure

 WriteBands  true

 BandLinesScale   pi/a

 %block Bandlines
 1 1.000 1.000 1.000 L
 25 0.000 0.000 0.000 \Gama
 30 2.000 0.000 0.000 X
 10 2.000 0.500 0.500 U
 35 0.000 0.000 0.000 \Gama
 %endblock block Bandlines

 The bands lines can be scaled by pi/a or Recipprocal Lattice Vectors. I
 think that it is more easy by ReciprocalLatticeVectors. But I think that
 according your data are scaled by pi/a.

 In systemlabel.bands are the bandlines. Then, you have to compile gnubands
 (utility directory): ./gnubands systemlabel.bands bandsoutput.
 Now, you have a file, use this file to plot bands stracture with gnuplots,
 xmgrace, sigmaplot, origin, matlab, ect.
 Coordinates of k points are at the end of systemlabel.bands and energy
 fermi are in the top of file.bands.


 As I said above, few weeks ago I had the same problem. I wrote to
 L-SIESTA, with the subject Band structure calculations and K-points,
 check it. It helps me a lot.




  Dear All,
 
  I am new user SIESTA. I would like to calculate the band structure 0f C80
  fullerene. Below I have written the input for the band structure and my
  results is showing just the straight line. Can any body tell me the what
  is
  wrong in my input? Please help how to use the X.band file for band
  structure?
 
  Thanks!
  SC
 
  %block BandLines
   1 1.000 1.000 1.000 L
  25 0.000 0.000 0.000 \Gama
  30 2.000 0.000 0.000 X
  10 2.000 0.500 0.500 U
  35 0.000 0.000 0.000 \Gama
  %endblock BandLines
 
  %block WaveFunKPoints
0.000 0.000 0.000 free 1 to 10
  %endblock WaveFuncKpoints
 

Re: [SIESTA-L] Band Structure

[sugata chowdhury]

Band structure of a fullerene C80.
SC

On Thu, Jan 28, 2010 at 3:05 PM, N H neyh...@gmail.com wrote:

 band structure of a molecule?

 cheers

 NH


 On Thu, Jan 28, 2010 at 7:51 PM, sugata chowdhury sugata2...@gmail.comwrote:

 Dear All,

 I am new user SIESTA. I would like to calculate the band structure 0f C80
 fullerene. Below I have written the input for the band structure and my
 results is showing just the straight line. Can any body tell me the what is
 wrong in my input? Please help how to use the X.band file for band
 structure?

 Thanks!
 SC

 %block BandLines
  1 1.000 1.000 1.000 L
 25 0.000 0.000 0.000 \Gama
 30 2.000 0.000 0.000 X
 10 2.000 0.500 0.500 U
 35 0.000 0.000 0.000 \Gama
 %endblock BandLines

 %block WaveFunKPoints
   0.000 0.000 0.000 free 1 to 10
 %endblock WaveFuncKpoints

Re: [SIESTA-L] Band Structure

[Marcos Veríssimo Alves]

Which is a molecule nonetheless. It just makes some sense, perhaps, if
we are talking about a molecular crystal, or if you are working with
the C80 molecules in a polymerized state. Otherwise, all you need ia a
gamma point calculation in a cell big enough to get your molecule
isolated, and look at the .EIG file for the discrete energy levels.

Marcos

On Thu, Jan 28, 2010 at 9:08 PM, sugata chowdhury sugata2...@gmail.com wrote:
 Band structure of a fullerene C80.
 SC

 On Thu, Jan 28, 2010 at 3:05 PM, N H neyh...@gmail.com wrote:

 band structure of a molecule?
 cheers
 NH

 On Thu, Jan 28, 2010 at 7:51 PM, sugata chowdhury sugata2...@gmail.com
 wrote:

 Dear All,

 I am new user SIESTA. I would like to calculate the band structure 0f C80
 fullerene. Below I have written the input for the band structure and my
 results is showing just the straight line. Can any body tell me the what is
 wrong in my input? Please help how to use the X.band file for band
 structure?

 Thanks!
 SC

 %block BandLines
  1 1.000 1.000 1.000 L
     25 0.000 0.000 0.000 \Gama
     30 2.000 0.000 0.000 X
     10 2.000 0.500 0.500 U
     35 0.000 0.000 0.000 \Gama
 %endblock BandLines

 %block WaveFunKPoints
   0.000 0.000 0.000 free 1 to 10
 %endblock WaveFuncKpoints

Re: [SIESTA-L] Band structure calculations and K-points

[gjgarcia]

Hi Marcos
Thank a lot,

Gregorio



 Hi Gregorio,

 On Thu, Jan 7, 2010 at 1:02 PM,  gjgar...@ujaen.es wrote:
 I am a new user of SIESTA.

 It's ok, everyone has been one at some point :D

 I am trying to calculated the band structure a
 pi-conjugated polymer. I have searched in the SIESTA-L, I have found
 that
 I need a blocklabel such as

 BandLinesScale  ReciprocalLatticeVectors

 %block BandLines
 1    0.0   0.0  0.0   # Gamma-point
 20  0.5   0.0  0.0   # X-point
 etc
 %endblock BandLines

 I have to add:
 WriteBands      True

 If the manual says so... (really, I don't remember it by heart).


 I have some questions:

 1)I noted that BandLinesScales can be scaled by ReciprocalLatticeVectors
 or pi/2, which is the differece?

 A huge one when it comes to specifying the points to be plotted, but
 the results are the same. For the first, you can determine at which
 points your band structure will be written as a fraction of the
 reciprocal lattice vectors themselves, whereas in the second, you will
 have actual cartesian coordinates in k-space, but scaled by the factor
 pi/a. As an example, suppose you have a 2D cell in real space with
 LatticeConstant A, such that


 LatticeConstant   A  Ang
 %block LatticeVectors
 1.000  0.000   0.000
 0.000  5.000   0.000
 0.000  0.000  50.000
 %endblock LatticeVectors

 The reciprocal lattice vectors as siesta calculates would then be

 b1=(2*pi/A,0) and b2=(0,2*pi/5A)

 (b3 is close to zero, so I won't take it into account from now on). So
 now suppose that the points of interest to you are the middle of the
 largest side **of the BZ** (let's call it M), one of its corners
 (let's call it Y), and the Gamma point. In the first case
 (ReciprocalLatticeVectors), these three coordinates can be written as

 Gamma=(0,0)
 M=(0.5,0)
 Y=(0.5,0.5)

 (remember that the Brillouin zone is the Wigner-Seitz cell in
 reciprocal space!). In the second case (scaled by pi/A), you'd have

 Gamma=(0,0)
 M=(1.,0)
 Y=(1.0,1/5)

 get it? It's just two different ways of expressing the same thing,
 whatever is easier for you. Often it is easier to use the fractional
 coordinates in k-space (ReciprocalLatticeVectors).


 2) The first colum indicates the grid between  two consecutive points.
 How
 Can I know what value Must I use?
 What k-points (gamma, x, L, etc) Must I use?

 Does it related with WirteKpoints, WreteEigenvalues and Writekbands?


 That depends on the symmetry of your system. In your case, plotting a
 band structure only makes sense if you have a crystal or an infinte
 polymer chain - in this latter case, all you have to do is plot the
 structure along the reciprocal lattice vector corresponding to the
 polymer chain's length. There are some internet resources on
 crystallography that give you a set of high-symmetry k-points for many
 lattices, I think the Bilbao Crystallographic Server is completely
 open for everyone.

 3) Finally. I know about GnuPlot, Does anyone tell me some program for
 view the band structures? Does some program for Windows operative
 system?

 Gnuplot for Windows? :) (It does exist...)

 Check the siesta documentation for the bands files, it's pretty
 straightforward to plot them using gnuplot.

 Marcos

Re: [SIESTA-L] Band structure calculations and K-points

[Christopher Rowan]

I prefer using xmgrace to plot band structures: menus and windows to change
plot settings...

Chris Rowan

2010/1/7 Mehmet Topsakal topsa...@unam.bilkent.edu.tr

 Hi Gregorio,

 for band structure plotting, you can follow these simple steps:

 Suppose that we have a carbon chain structure as in RUN.fdf attachment.
 After running siesta as siesta  RUN.fdf  OUT.fdf , Chain.bands file
 will be generated. Copy the draw_bands script into your $HOME/bin
 directory and make it executable. Then call it as draw_bands OUT.fdf -5
 +5 from linux terminal. Here OUT.fdf is the output file which is
 generated after siesta run and -5 and +5 are the y-axis energy boundaries
 for band structure plot.

 draw_bands script requires 2 external programs. The first one is
 gnubands.x which can be found in /Utils/ directory of siesta setup. It can
 easily be compiled by f95, ifort, gfortran The second one is matlab
 (or octave). Octave setup is very easy in linux. Simply type apt-get
 install octave or yum install octave from terminal for ubuntu and
 fedora.

 draw_bands generates two files, bands.dat2 and bands.m . You can copy them
 to your windows machine and run bands.m with matlab. Matlab figures look
 better and i prefer to use matlab. But octave figures are also sufficient.

 These procedure is really easy and produces a nice band structure plot as
 shown in attachment (bands.eps or bands.pdf). All subplots are the same
 band structure with different y-axis limits. The fermi level is shifted to
 the zero and the band gap (Eg) is also calculated as seen from the eps
 file.

 I suggest you to examine the 85. 86. 87. 99. 100. 101. lines of
 draw_bands script and modify them as you wish.

 I hope these help you.




  2010/1/7 Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com
  Hi Gregorio,


  On Thu, Jan 7, 2010 at 1:02 PM,  gjgar...@ujaen.es wrote:
   I am a new user of SIESTA.


 It's ok, everyone has been one at some point :D


   I am trying to calculated the band structure a
   pi-conjugated polymer. I have searched in the SIESTA-L, I have found
 that
   I need a blocklabel such as
  
   BandLinesScale  ReciprocalLatticeVectors
  
   %block BandLines
   10.0   0.0  0.0   # Gamma-point
   20  0.5   0.0  0.0   # X-point
   etc
   %endblock BandLines
  
   I have to add:
   WriteBands  True


 If the manual says so... (really, I don't remember it by heart).


  
   I have some questions:
  
   1)I noted that BandLinesScales can be scaled by ReciprocalLatticeVectors
   or pi/2, which is the differece?


 A huge one when it comes to specifying the points to be plotted, but
  the results are the same. For the first, you can determine at which
  points your band structure will be written as a fraction of the
  reciprocal lattice vectors themselves, whereas in the second, you will
  have actual cartesian coordinates in k-space, but scaled by the factor
  pi/a. As an example, suppose you have a 2D cell in real space with
  LatticeConstant A, such that


  LatticeConstant   A  Ang
  %block LatticeVectors
  1.000  0.000   0.000
  0.000  5.000   0.000
  0.000  0.000  50.000
  %endblock LatticeVectors

  The reciprocal lattice vectors as siesta calculates would then be

  b1=(2*pi/A,0) and b2=(0,2*pi/5A)

  (b3 is close to zero, so I won't take it into account from now on). So
  now suppose that the points of interest to you are the middle of the
  largest side **of the BZ** (let's call it M), one of its corners
  (let's call it Y), and the Gamma point. In the first case
  (ReciprocalLatticeVectors), these three coordinates can be written as

  Gamma=(0,0)
  M=(0.5,0)
  Y=(0.5,0.5)

  (remember that the Brillouin zone is the Wigner-Seitz cell in
  reciprocal space!). In the second case (scaled by pi/A), you'd have

  Gamma=(0,0)
  M=(1.,0)
  Y=(1.0,1/5)

  get it? It's just two different ways of expressing the same thing,
  whatever is easier for you. Often it is easier to use the fractional
  coordinates in k-space (ReciprocalLatticeVectors).


  
   2) The first colum indicates the grid between  two consecutive points.
 How
   Can I know what value Must I use?
   What k-points (gamma, x, L, etc) Must I use?
  
   Does it related with WirteKpoints, WreteEigenvalues and Writekbands?
  


 That depends on the symmetry of your system. In your case, plotting a
  band structure only makes sense if you have a crystal or an infinte
  polymer chain - in this latter case, all you have to do is plot the
  structure along the reciprocal lattice vector corresponding to the
  polymer chain's length. There are some internet resources on
  crystallography that give you a set of high-symmetry k-points for many
  lattices, I think the Bilbao Crystallographic Server is completely
  open for everyone.


   3) Finally. I know about GnuPlot, Does anyone tell me some program for
   view the band structures? Does some program for Windows operative
 system?


 Gnuplot for Windows? :) (It does exist...)

  Check the siesta