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Clarification on ESM
Date: 2020/09/11 03:48
Name: Mauro Sgroi   <mauro.sgroi@crf.it>

Dear all,
I'm writing to ask for a clarification about ESM.
Using it with a graphene monolayer with the a 6x6 supercell:

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
14.754317305999999 0.000000000000000 0.000000000000000
-7.377162205000000 12.777619736000000 0.000000000000000
0.000000000000000 0.000000000000000 20.000000000000000
Atoms.UnitVectors>


I get the following error:

<ESM:Warning>
The b- and c-axes of the unit cell used for the ESM calculation
must be orthogonal to the a-axis.

I'm using

ESM.switch on1
ESM.buffer.range 2.0
ESM.direction z

So, has the cell to be orthorombic to use ESM?


Thanks a lot in advance and best regards,

Mauro Sgroi.

Centro Ricerche FIAT
Italy
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Re: Clarification on ESM ( No.1 )
Date: 2020/09/11 12:16
Name: Naoya Yamaguchi

Hi,

As the warning says, you have to set the a-axis orthogonal to the b- and c-axes. "ESM.direction" seems to choose a Cartesian axis for the ESM direction, not a cell axis. So, the a-axis is always taken as a special axis for the ESM, and you may avoid it by
<Atoms.UnitVectors
0.000000000000000 0.000000000000000 20.000000000000000
14.754317305999999 0.000000000000000 0.000000000000000
-7.377162205000000 12.777619736000000 0.000000000000000
Atoms.UnitVectors>
if the structure is the same as in http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2677

Regards,
Naoya Yamaguchi
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Re: Clarification on ESM ( No.2 )
Date: 2020/09/14 19:11
Name: Mauro Sgroi  <mauro.sgroi@crf.it>

Dear Naoya,
thanks a lot.
I'm using ESM.direction z.
So I was expecting to be able to use the c-axis instead of the a-axis.
Is it not the case?
Best regards,
Mauro Sgroi.
メンテ
Re: Clarification on ESM ( No.3 )
Date: 2020/09/15 03:27
Name: Naoya Yamaguchi

Dear Mauro,

>So I was expecting to be able to use the c-axis instead of the a-axis.
I also expected that, but the written source code was not true of it.

Regards,
Naoya Yamaguchi
メンテ
Re: Clarification on ESM ( No.4 )
Date: 2020/09/18 18:40
Name: Mauro Sgroi  <maurofrancesco.sgroi@gmail.com>

Dear Naoya,
thanks a lot!
Can I ask a further clarification?
I don't understand fully how to use ESM.buffer.range.

I've a cell with an height of 30 Ang and a graphene monolayer at 7.5 Ang.
The vacuum of the cell on top to will be filled with solvent molecules.

Should I fix ESM.buffer.range to 30 Ang so that it covers the full supercell?

Thanks a lot and best regards,
Mauro.
メンテ
Re: Clarification on ESM ( No.5 )
Date: 2020/09/19 02:34
Name: Naoya Yamaguchi

Dear Mauro,

"ESM.buffer.range" is no longer active as I checked the source code.
As such, you need to avoid overlap between PAOs and the ESM by checking all the atomic coordinates manually.

>I've a cell with an height of 30 Ang and a graphene monolayer at 7.5 Ang.
>The vacuum of the cell on top to will be filled with solvent molecules.

You can use "ESM.wall.position" and "ESM.wall.height" to set barrier potential for restricting liquid molecules within a given region. Please take a look at "5. In case of MD calculations with the ESM method:" in http://www.openmx-square.org/openmx_man3.9/node151.html

Regards,
Naoya Yamaguchi
メンテ
Re: Clarification on ESM ( No.6 )
Date: 2020/09/20 05:33
Name: Mauro Sgroi  <maurofrancesco.sgroi@gmail.com>

Dear Naoya,
many thanks for the help.
Best regards,
Mauro Sgroi.
メンテ
Re: Clarification on ESM ( No.7 )
Date: 2020/09/24 18:33
Name: Mauro Sgroi  <maurofrancesco.sgroi@gmail.com>

Dear all,
I use this thread to ask a further question on ESM.
If I want to simulate a charged electrode I've to use ESM.switch = on3 and set the charge using scf.system.charge.

But I add solvent molecules all the supercell will be charged so I cannot simulate the fact that the charge is on the slab and that there is a potential difference between the solid and the electrolyte.

Is there a way to proceed?

Any published reference that can help?


Thanks a lot in advance and best regards,

Mauro Sgroi.
メンテ
Re: Clarification on ESM ( No.8 )
Date: 2020/10/07 23:26
Name: Mauro Sgroi  <maurofrancesco.sgroi@gmail.com>

Dear developers,
I discussed with Dr. Sugino the fact that in ESM it is possible to add a confinement potential to prevent electrons from leaking out from the conducting slab.
This is described in the papers below:

doi:10.1016/j.susc.2007.04.208

DOI:10.1143/JPSJ.77.024802

Is this functionality implemented in Openmx?

Thanks a lot and best regards,
Mauro Sgroi.
メンテ
Re: Clarification on ESM ( No.9 )
Date: 2020/10/08 13:12
Name: Naoya Yamaguchi

Dear Mauro,

Although I'm not the developer of the ESM function, as I checked the source code files, the artificial potential appears only in the calculation of atomic forces. There doesn't seem to be such a direct confinement potential for electrons, but OpenMX uses the numerical localized orbitals of PAOs as the basis set. So, I think that electrons may be naturally confined due to the cutoff radii of PAOs.

Regards,
Naoya Yamaguchi
メンテ
Re: Clarification on ESM ( No.10 )
Date: 2020/10/08 17:52
Name: Mauro Sgroi  <maurofrancesco.sgroi@gmail.com>

Dear Naoya,
thanks a lot for the clarification.
Best regards,
Mauro.
メンテ

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