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