Re: [SIESTA-L] << Increasing RHO mesh >>

[I. Camps]

Hello Nick,

My input file is below. I duplicate the grid size.

Also, I save the output from DENCHAR to a file and keep monitoring the CPU
and memory usage.

In the output there is no indication of error and the memory usage keep
above 4GB with a 49% use (my note have 8GB).

### INPUT
SystemLabel BN-Ni-p4-dCRITIC2
NumberOfSpecies3
%block ChemicalSpeciesLabel
  1   5  B
  2   7  N
  3  28  Ni
%endblock ChemicalSpeciesLabel
Denchar.TypeOfRun  3D
Denchar.PlotCharge T
Denchar.CoorUnits   Ang   # Format for coordinate of the points
   # Bohr
   # Ang
Denchar.DensityUnits   Ele/Ang**3 # Units of Charge Density
   # Ele/bohr**3
   # Ele/Ang**3
   # Ele/UnitCell
Denchar.NumberPointsX  480
Denchar.NumberPointsY  480
Denchar.NumberPointsZ  360

Denchar.MinX  0  Ang
Denchar.MaxX  17.833623 Ang
Denchar.MinY  0 Ang
Denchar.MaxY  17.833623  Ang
Denchar.MinZ  0  Ang
Denchar.MaxZ  12.171076 Ang
###

### OUTPUT
...
...
 115 23.089612.3513 2.6562
   116 23.041412.373710.7105
   117 23.060412.365518.7637
   118 24.088814.5243 1.3261
   119 24.059614.5373 9.3802
   120 24.062314.539317.4349
   121 14.8510 5.857515.3723

   Generating Charge Density values on the grid now
   Please, wait
###


Regards,

Camps


On Wed, Apr 7, 2021 at 5:17 PM Nick Papior  wrote:

> Hi,
>
> Hmm.. That depends on the options you use. It could be that you run out of
> memory?
> Perhaps some more information about what was before this would be useful?
> I.e. what does denchar print before writing "Killed"?
>
> Den tor. 1. apr. 2021 kl. 22.02 skrev I. Camps :
>
>> Thank you very much Nick!
>>
>> I am using the second option...
>>
>> The original mesh is 240x240x180. I tried to double it, but DENCHAR just
>> stopped with a simple text: "Killed", without any information about.
>>
>> Do you have a recommendation about the best form to select the grid?
>>
>> []'s,
>>
>> Camps
>>
>>
>> On Mon, Mar 29, 2021 at 5:02 PM Nick Papior  wrote:
>>
>>> Hi,
>>>
>>> You can use sisl to interpolate and write out the a cube file.
>>>
>>> For instance,
>>>
>>> sgrid siesta.RHO --interp 300 400 400 --out rho.cube
>>>
>>> will interpolate the RHO grid to a size of 300, 400, 400, x, y, z
>>> directions. Please refer to sgrid --help for more information. For instance
>>> the interpolation method may be quite important in your case.
>>>
>>> Alternatively you can use denchar to replot the density matrix files
>>> using a denser grid. This is of course more precise since it isn't
>>> interpolation but using the same DM to recreate the full grid on a
>>> different mesh.
>>>
>>> Good luck!
>>>
>>> Den søn. 28. mar. 2021 kl. 23.01 skrev I. Camps :
>>>
 Dear SIESTers,

 I am doing a critical point study using the package CRITIC2, but for
 SIESTA, it only accepts the RHO density in cube format, so its results are
 dependent on the quality of the used grid.

 Is it possible to increase the mesh for the grid where RHO is
 calculated?

 []'s,

 Camps

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

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

-- 
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] extracting band gap from EIG file

[Nick Papior]

Yes. That could be done.

Den tor. 8. apr. 2021 kl. 22.03 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:

> Oh in that case then I just have to go through the band structure. Then I
> go through the EIG file to find the exact values.
>
> Is that correct?
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
> *From: *Nick Papior 
> *Sent: *Thursday, 8 April 2021 6:06 AM
> *To: *siesta-l 
> *Subject: *Re: [SIESTA-L] extracting band gap from EIG file
>
>
>
> This depends on which bandgap you want?
>
>
>
> 1) An indirect bandgap
>
> Here you should take the lowest unoccupied state for *all* kpoints, and
> the highest occupied state for *all* kpoints. Then the difference between
> the two is the indirect bandgab.
>
> 2) A direct bandgap
>
> Here you should take the lowest unoccupied state for ONE kpoint, and the
> highest occupied state for the same kpoint. The difference between the two
> is the direct bandgap for that k-point. You then repeat this for *all*
> kpoints and take the lowest one of them all. That is the direct bandgap.
>
>
>
> Note however, that it is important you have a sufficiently dense kgrid to
> get reasonable results. This is of course material dependent.
>
>
>
>
>
>
>
> Den ons. 31. mar. 2021 kl. 22.04 skrev El-abed Haidar <
> ehai2...@uni.sydney.edu.au>:
>
> Good afternoon,
>
>1. I was wondering if I want to extract the bandgap other than from
>the PDOS, is it possible to do so from the EIG file?
>2. I heard it before but I am not sure by looking at the different k
>points in the EIG file, which k pt to choose? Is it based on the band
>structure and closest to the Fermi energy?
>
> Thank you and looking forward to everyones’ thoughts
>
> Thank you,
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/
> 
> )
>
>
>
>
> --
>
> Kind regards Nick
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 
Kind regards Nick

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