RE: [SIESTA-L] FW: Concerning Denchar

[El-abed Haidar]

Hello Nick, Thank you for the reply:



  1.  Sisl can do what denchar can? That’s fantastic, I was wondering how 
because I will give you my feedback 
  2.  Can you let me know how though? As far I understand, sisl is made of 3 
parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation is to use 
sgrid. Then the real questions are:
  3.  Which nc file should I use to get the homo and lumo as in denchar?
  4.  Is there a specific sisl page tutorial for such?
  5.  What are the main sisl commands that would be equivalent to: denchar -k 3 
-w 4  file.fdf  ??
  6.  Since there is no GitHub for denchar and since I could not find the 
command in the denchar manual, where can I find the commands mentioned in 4??

Thank you and eager to reading your reply.
EL-abed

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: Saturday, 16 January 2021 8:02 AM
To: siesta-l
Subject: Re: [SIESTA-L] FW: Concerning Denchar

Hmm.

Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 
mailto:ehai2...@uni.sydney.edu.au>>:
Good evening,

  1.  I was wondering if Denchar has problems with systems which are not 
orthorhombic as it was in 1.3 version? Because when I studied a molecule inside 
orthorhombic system, I could visualize cube files. When I study for example 
graphene in an hexagonal system, even though the file is not empty (13000 kb) I 
could not visualize it.
I am pretty sure it works for other than orthorhombic cells. However, the 
output can only be in an orthorhomic cell.

  1.
  2.  Does Denchar have its own GitHub like sisl? Alberto once gave a great 
advice of using denchar -k 3 -w 4  file.fdf  which will plot only the 
wave-function with (original) index 4 of the third  k-point in the (WFSX) file. 
An
No, denchar is part of the siesta distribution.
sisl can in principle do what denchar does, however it is not as tested as 
denchar (so any feedback on them would be really nice!)

  1.
  2.  May I convert the output cube file to xsf files in siesta?
You can do this with sisl

sgrid input.cube output.xsf
or
sdata input.cube output.xsf

Denchar does not write out xsf files.

  1.

Thank you and looking forward to your reply.
EL-abed

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/)

[SIESTA-L] Denchar command "denchar -k 3 -w 4 file.fdf " not working ?

[El-abed Haidar]

Good evening,
I was trying to use dencar command denchar -k 3 -w 4  file.fdf  which will plot 
only the wave-function with (original) index 4 of the third  k-point in the 
(WFSX) file.
But when I tried to use it in denchar 2.2 it just would not go through the 
specified k point nor wave function.
Is there a reason??
Here is my proof in the update file where I used the command : denchar -k 3 -w 
4  file.fdf >update.txt.
Denchar works but not as commanded
Any advice ?
Thank you and looking forward to your reply.
EL-abed

El-abed Haidar | Doctor of Philosophy (Science)
 Condensed Matter Theory (CMT) Group| School of Physics
 THE UNIVERSITY OF SYDNEY  | NSW | 2006

sSpecies number:   1 Atomic number:   15 Label: P
Species number:   2 Atomic number:6 Label: C
 

iodm: Reading Density Matrix from file
     
  *  WELCOME TO DENCHAR  *   
     
  DENCHAR version: 2.2
  You are running DENCHAR for system: zeroPG
  

  You have chosen the 3D mode. Values of the functions
  will be given in a 3D grid, in Gaussian Cube format

  Number of points in the x-direction : 
100
  Number of points in the y-direction : 
100
  Number of points in the z-direction : 
100
  Minimum value of the x-component of the window : 
   0.0 bohrs
  Maximum value of the x-component of the window : 
  18.89727 bohrs
  Minimum value of the y-component of the window : 
   0.0 bohrs
  Maximum value of the y-component of the window : 
 115.27334 bohrs
  Minimum value of the z-component of the window : 
   0.0 bohrs
  Maximum value of the z-component of the window : 
  37.79454 bohrs
  
  The options you have chosen to generate the plane
  are the following: 
  
  Option to generate the plane : NormalVector
  Components of the normal vector : 
   0.0 0.0 1.0
  Origin of the plane : 
   0.0 0.0 0.0
  Another point to define the X direction : 
   1.88973 0.0 0.0
  
  Unit of the charge density in output files : 
  Electrons/(bohr**3)
  
  Atomic coordinates in the in-plane reference frame
  Atomic Index   Atomic coordinates
 1  6.2320 3.626128.3638
 2  6.230812.367228.3635
 3  6.227821.101428.3553
 4  6.232329.820128.3490
 5  6.233038.544728.3638
 6  6.234247.286928.3829
 7  6.235956.047428.3727
 8  6.237964.793928.3439
 9  6.238573.512528.3402
10  6.237182.234628.3595
11  6.235890.971528.3730
12  6.234399.722528.3714
13  6.2329   108.466928.3605
14 12.4706 3.624628.3668
15 12.470912.364628.3644
16 12.467221.102728.3588
17 12.469729.823728.3532
18 12.467438.546028.3672
19 12.466147.288428.3876
20 12.464756.050028.3778
21 12.466264.793828.3457
22 12.466173.513828.3413
23 12.466382.235628.3615
24 12.467690.972628.3751
25 12.468999.723828.3745
26 12.4702   108.468328.3635
27 18.6986 3.622628.3613
28 18.699812.365328.3536
29 18.705929.823428.3416
30 18.703638.548128.3588
31 18.701447.292228.3795
32 18.700756.051828.3760
33 18.697764.795328.3535
34 18.696973.512628.3527
35 18.696982.233428.3712
36 18.696890.969328.3844
37 18.697099.720228.3784
38 18.6974   108.464128.3644
39 18.7000 5.092224.2208
40 18.699357.509324.2313
41 18.697866.246224.2066
42